[AMBER-Developers] Proposing amber10 bugfix on PBSA

From: MengJuei Hsieh <mengjueh.uci.edu>
Date: Thu, 16 Jul 2009 05:29:11 +0100

Hi

This is a proposed bugfix for Amber10 PBSA with following descriptions, some
test cases for pbsa would be also updated. Please note that I used two frinsic functions ceiling() and floor(), hopefully this works out for
every.

Thanks!
-- Mengjuei Hsieh, Molecular Biology & Biochem, Univ. of Californe.

********>Bugfix 23:
Author: Meng-Juei Hsieh & Xiang Ye

Date: July 15, 2009

Programs: pbsa

Description:
     1. In a large system, variable maxmax may overflow due to the limit
        of integer. (in is_init.f)
     2. In some cases int(myfloat)+1 and int(myfloat) are not correct if the
        value of myfloat is negative. (in pb_exmol.f and pb_force.f)
     3. Two unsigned variables randomly causing different print-outs in
        dynlib.f.
     4. The variable "small" is not small enough to produce correct result
        in sa_driver.f

Use this patch to update under amber10 directory.
----------------------------------------------------------------------------
Index: src/pbsa/is_init.f
===================================================================
--- src/pbsa/is_init.f (original)
+++ src/pbsa/is_init.f (working copy)
.@ -530,7 +530,12 @@

    maxnba = natom * ( sqrt( max(cutnb,cutsa,cutfd) ) )**3 / 3.0d0
    maxnbr = natom * ( sqrt( cutres ) + 3.0d0 )**3 / 3.0d0
- maxmax = int(REAL(natom*natom)/2) + 1
+ if ( natom >= 65536 ) then
+ write(6,'(a)') "PB Warnning: natom**2 exceeds integer limit
(2147483647)."
+ maxmax = 2147483647
+ else
+ maxmax = ceiling(REAL(natom)/2*REAL(natom))
+ endif
    if ( maxnba > maxmax ) maxnba = maxmax
    if ( maxnbr > maxmax ) maxnbr = maxmax
    allocate( iar1pb (6,0:natom), stat = alloc_err(24) )
Index: src/pbsa/pb_exmol.f
===================================================================
--- src/pbsa/pb_exmol.f (original)
+++ src/pbsa/pb_exmol.f (working copy)
.@ -141,17 +141,17 @@

    r = rh*radi(iatm)

- lowk = int(zi - range1) + 1; highk = int(zi + range1)
+ lowk = ceiling(zi - range1); highk = floor(zi + range1)
    do k = lowk, highk

       range2 = sqrt(range1**2-(zi-REAL(k))**2)
- lowj = int(yi - range2) + 1; highj = int(yi + range2)
+ lowj = ceiling(yi - range2); highj = floor(yi + range2)
       do j = lowj, highj

          range3 = sqrt(range2**2-(yi-REAL(j))**2)
          if ( range3 > ZERO ) then

- lowi = int(xi - range3) + 1; highi = int(xi + range3)
+ lowi = ceiling(xi - range3); highi = floor(xi + range3)
             do i = lowi, highi
                d2 = (i-xi)**2 + (j-yi)**2 + (k-zi)**2; d = sqrt(d2)
                if ( d > r ) then
.@ -204,17 +204,17 @@
    integer highi, highj, highk
    _REAL_ range2, range3, d2

- lowk = int(zi - range1) + 1; highk = int(zi + range1)
+ lowk = ceiling(zi - range1); highk = floor(zi + range1)
    do k = lowk, highk

       range2 = sqrt(range1**2-(zi-REAL(k))**2)
- lowj = int(yi - range2) + 1; highj = int(yi + range2)
+ lowj = ceiling(yi - range2); highj = floor(yi + range2)
       do j = lowj, highj

          range3 = sqrt(range2**2-(yi-REAL(j))**2)
          if ( range3 > ZERO ) then

- lowi = int(xi - range3) + 1; highi = int(xi + range3)
+ lowi = ceiling(xi - range3); highi = floor(xi + range3)
             do i = lowi, highi
                d2 = (i-xi)**2 + (j-yi)**2 + (k-zi)**2
                if ( insph(i,j,k) == dielsph ) then
.@ -334,17 +334,17 @@
    integer highi, highj, highk
    _REAL_ range2, range3, d2

- lowk = int(zi - range1) + 1; highk = int(zi + range1)
+ lowk = ceiling(zi - range1); highk = floor(zi + range1)
    do k = lowk, highk

       range2 = sqrt(range1**2-(zi-REAL(k))**2)
- lowj = int(yi - range2) + 1; highj = int(yi + range2)
+ lowj = ceiling(yi - range2); highj = floor(yi + range2)
       do j = lowj, highj

          range3 = sqrt(range2**2-(yi-REAL(j))**2)
          if ( range3 > ZERO ) then

- lowi = int(xi - range3) + 1; highi = int(xi + range3)
+ lowi = ceiling(xi - range3); highi = floor(xi + range3)
             do i = lowi, highi
                if ( insph(i,j,k) == -2 ) cycle
                d2 = (i-xi)**2 + (j-yi)**2 + (k-zi)**2
Index: src/pbsa/dynlib.f
===================================================================
--- src/pbsa/dynlib.f (original)
+++ src/pbsa/dynlib.f (working copy)
.@ -231,6 +231,11 @@
 # include "files.h"
 # include "md.h"
    dimension ener(*),fac(*)
+
+ ! ----- PBSA DOESN'T NEED THIS -----
+
+ induced = 0
+ indmeth = 0

    ! ----- DEFINE VARIOUS TERMS -----

Index: src/pbsa/sa_driver.f
===================================================================
--- src/pbsa/sa_driver.f (original)
+++ src/pbsa/sa_driver.f (working copy)
.@ -679,7 +679,7 @@
    integer nsrf, nsurf
    integer fstsph(natom), lstsph(natom)
    _REAL_ sx, sy, sz, xi, yi, zi, dx, dy, dz, dxij, dyij, dzij, d2
- _REAL_, parameter :: small = 0.001d0
+ _REAL_, parameter :: small = 0.0001d0

    allocate(knockout( maxsph*natom), stat = alloc_err(1) )
    allocate( sphcrd(3,maxsph*natom), stat = alloc_err(2) )
Index: src/pbsa/pb_force.f
===================================================================
--- src/pbsa/pb_force.f (original)
+++ src/pbsa/pb_force.f (working copy)
.@ -406,12 +406,12 @@
          gcrd(3,iatm) = (acrd(3,iatm) - goz)*rh
       end do
       do iatm = 1, natom
- icrd(1,iatm) = int(gcrd(1,iatm))
- icrd(2,iatm) = int(gcrd(2,iatm))
- icrd(3,iatm) = int(gcrd(3,iatm))
- fcrd(1,iatm) = REAL(icrd(1,iatm))
- fcrd(2,iatm) = REAL(icrd(2,iatm))
- fcrd(3,iatm) = REAL(icrd(3,iatm))
+ icrd(1,iatm) = floor(gcrd(1,iatm))
+ icrd(2,iatm) = floor(gcrd(2,iatm))
+ icrd(3,iatm) = floor(gcrd(3,iatm))
+ fcrd(1,iatm) = REAL(icrd(1,iatm))
+ fcrd(2,iatm) = REAL(icrd(2,iatm))
+ fcrd(3,iatm) = REAL(icrd(3,iatm))
       end do
       do iatm = 1, natom
          aa = gcrd(1,iatm) - fcrd(1,iatm)
Index: test/pbsa_pgb/mdout.pbpgb.min.save
===================================================================
--- test/pbsa_pgb/mdout.pbpgb.min.save (original)
+++ test/pbsa_pgb/mdout.pbpgb.min.save (working copy)
.@ -3,7 +3,7 @@
           Amber 9 PBSA Scripps/UCSF 2006
           -------------------------------------------------------

-| Run on 12/10/2005 at 17:48:03
+| Run on 07/15/2009 at 12:34:10
   [-O]verwriting output

 File Assignments:
.@ -107,8 +107,8 @@

  Total surface charge 3.9570
  Reaction field energy -965.9273
- Cavity solvation energy 162.4615
- Dispersion solvation energy -186.7203
+ Cavity solvation energy 162.4459
+ Dispersion solvation energy -186.6934


    NSTEP ENERGY RMS GMAX NAME NUMBER
.@ -117,7 +117,7 @@
  BOND = 15.9232 ANGLE = 72.0306 DIHED =
259.6946
  VDWAALS = -427.2541 EEL = -4439.9066 EPB =
-965.9273
  1-4 VDW = 182.2148 1-4 EEL = 3058.2617 RESTRAINT =
0.0000
- ECAVITY = 162.4615 EDISPER = -186.7203
+ ECAVITY = 162.4459 EDISPER = -186.6934


   Maximum number of minimization cycles reached.
.@ -133,34 +133,34 @@
  BOND = 15.9232 ANGLE = 72.0306 DIHED =
259.6946
  VDWAALS = -427.2541 EEL = -4439.9066 EPB =
-965.9273
  1-4 VDW = 182.2148 1-4 EEL = 3058.2617 RESTRAINT =
0.0000
- ECAVITY = 162.4615 EDISPER = -186.7203
+ ECAVITY = 162.4459 EDISPER = -186.6934

 ---------------------------------------------------------------------------
-----
    5. TIMINGS
 ---------------------------------------------------------------------------
-----

-| Read coords time 0.00 ( 0.07% of Total)
-| PB NB list 0.03 ( 0.64% of PB No)
-| PB FD grid 0.39 ( 8.42% of PB No)
-| PB Epsmap 0.48 (11.56% of PB FD)
-| PB Solver 2.26 (54.53% of PB FD)
-| Other 1.41 (33.91% of PB FD)
-| PB FD Force 4.15 (89.83% of PB No)
-| PB Direct 0.05 ( 1.11% of PB No)
-| PB Nonbond 4.62 (66.90% of Nonbo)
-| NP Sasa 0.80 (35.10% of NP No)
-| NP Dispersion 1.48 (64.90% of NP No)
-| NP Nonbond 2.29 (33.10% of Nonbo)
-| Nonbond force 6.90 (100.0% of Force)
-| Bond/Angle/Dihedral 0.00 ( 0.06% of Force)
-| Force time 6.91 (100.0% of Runmd)
-| Runmd Time 6.91 (98.84% of Total)
-| Other 0.08 ( 1.09% of Total)
-| Total time 6.99 (100.0% of ALL )
+| Read coords time 0.01 ( 0.40% of Total)
+| PB NB list 0.01 ( 0.53% of PB No)
+| PB FD grid 0.13 ( 8.19% of PB No)
+| PB Epsmap 0.16 (10.98% of PB FD)
+| PB Solver 0.90 (61.47% of PB FD)
+| Other 0.40 (27.55% of PB FD)
+| PB FD Force 1.46 (90.07% of PB No)
+| PB Direct 0.02 ( 1.21% of PB No)
+| PB Nonbond 1.63 (68.64% of Nonbo)
+| NP Sasa 0.27 (35.84% of NP No)
+| NP Dispersion 0.48 (64.15% of NP No)
+| NP Nonbond 0.74 (31.36% of Nonbo)
+| Nonbond force 2.37 (100.0% of Force)
+| Bond/Angle/Dihedral 0.00 ( 0.04% of Force)
+| Force time 2.37 (100.0% of Runmd)
+| Runmd Time 2.37 (96.77% of Total)
+| Other 0.07 ( 2.82% of Total)
+| Total time 2.45 (100.0% of ALL )

 | Highest rstack allocated: 0
 | Highest istack allocated: 0
-| Job began at 17:48:03.641 on 12/10/2005
-| Setup done at 17:48:03.707 on 12/10/2005
-| Run done at 17:48:10.632 on 12/10/2005
+| Job began at 12:34:10.793 on 07/15/2009
+| Setup done at 12:34:10.863 on 07/15/2009
+| Run done at 12:34:13.241 on 07/15/2009
 | wallclock() was called 46 times
Index: test/pbsa_radi/out.save/probk.out.save
===================================================================
--- test/pbsa_radi/out.save/probk.out.save (original)
+++ test/pbsa_radi/out.save/probk.out.save (working copy)
.@ -3,7 +3,7 @@
           Amber 9 PBSA Scripps/UCSF 2006
           -------------------------------------------------------

-| Run on 12/10/2005 at 17:24:36
+| Run on 07/15/2009 at 12:34:16
   [-O]verwriting output

 File Assignments:
.@ -31,11 +31,11 @@
    igb=10, ntb=0,
    ntc=1, ntf=1, tol=0.000001,
    ntt=0, temp0=300
- /
+ /
  &pb
    npbverb=0, epsout=80.0, radiopt=1, space=0.5,
    accept=1e-4, fillratio=6, sprob=1.6
- /
+ /

 ---------------------------------------------------------------------------
-----
    1. RESOURCE USE:
.@ -109,17 +109,17 @@

  Total surface charge 0.0000
  Reaction field energy -17.5263
- Cavity solvation energy 16.9413
- Dispersion solvation energy -16.2003
+ Cavity solvation energy 16.9293
+ Dispersion solvation energy -16.1906


    NSTEP ENERGY RMS GMAX NAME NUMBER
- 1 -2.8167E+00 9.7868E+00 3.1030E+01 CB 14
+ 1 -2.8191E+00 9.7868E+00 3.1030E+01 CB 14

  BOND = 0.6004 ANGLE = 6.1334 DIHED =
16.9632
  VDWAALS = 3.1820 EEL = -74.1076 EPB =
-17.5263
  1-4 VDW = 5.6206 1-4 EEL = 55.5766 RESTRAINT =
0.0000
- ECAVITY = 16.9413 EDISPER = -16.2003
+ ECAVITY = 16.9293 EDISPER = -16.1906


   Maximum number of minimization cycles reached.
.@ -130,44 +130,43 @@


    NSTEP ENERGY RMS GMAX NAME NUMBER
- 1 -2.8167E+00 9.7868E+00 3.1030E+01 CB 14
+ 1 -2.8191E+00 9.7868E+00 3.1030E+01 CB 14

  BOND = 0.6004 ANGLE = 6.1334 DIHED =
16.9632
  VDWAALS = 3.1820 EEL = -74.1076 EPB =
-17.5263
  1-4 VDW = 5.6206 1-4 EEL = 55.5766 RESTRAINT =
0.0000
- ECAVITY = 16.9413 EDISPER = -16.2003
+ ECAVITY = 16.9293 EDISPER = -16.1906

 ---------------------------------------------------------------------------
-----
    5. TIMINGS
 ---------------------------------------------------------------------------
-----

-| Read coords time 0.00 ( 0.21% of Total)
+| Read coords time 0.00 ( 0.42% of Total)
 | Fast Water setup 0.00 ( 0.01% of Total)
 | PB NB list 0.00 ( 0.05% of PB No)
-| PB FD grid 0.00 ( 2.43% of PB No)
-| PB Epsmap 0.01 (10.56% of PB FD)
-| PB Solver 0.10 (87.50% of PB FD)
-| Other 0.00 ( 1.93% of PB FD)
-| PB FD Force 0.11 (97.46% of PB No)
-| PB Direct 0.00 ( 0.03% of PB No)
-| Other 0.00 ( 0.03% of PB No)
-| PB Nonbond 0.11 (93.41% of Nonbo)
-| NP Sasa 0.01 (66.43% of NP No)
-| NP Cavity 0.00 ( 0.60% of NP No)
-| NP Dispersion 0.00 (32.67% of NP No)
-| Other 0.00 ( 0.30% of NP No)
-| NP Nonbond 0.01 ( 6.59% of Nonbo)
-| Nonbond force 0.12 (99.79% of Force)
+| PB FD grid 0.00 ( 3.28% of PB No)
+| PB Epsmap 0.01 (13.12% of PB FD)
+| PB Solver 0.04 (84.55% of PB FD)
+| Other 0.00 ( 2.32% of PB FD)
+| PB FD Force 0.05 (96.62% of PB No)
+| PB Direct 0.00 ( 0.04% of PB No)
+| Other 0.00 ( 0.01% of PB No)
+| PB Nonbond 0.05 (91.32% of Nonbo)
+| NP Sasa 0.00 (67.92% of NP No)
+| NP Cavity 0.00 ( 0.14% of NP No)
+| NP Dispersion 0.00 (31.90% of NP No)
+| Other 0.00 ( 0.04% of NP No)
+| NP Nonbond 0.00 ( 8.68% of Nonbo)
+| Nonbond force 0.06 (99.81% of Force)
 | Bond/Angle/Dihedral 0.00 ( 0.19% of Force)
-| Other 0.00 ( 0.02% of Force)
-| Force time 0.12 (100.0% of Runmd)
-| Runmd Time 0.12 (92.02% of Total)
-| Other 0.01 ( 7.76% of Total)
-| Total time 0.13 (100.0% of ALL )
+| Force time 0.06 (100.0% of Runmd)
+| Runmd Time 0.06 (68.21% of Total)
+| Other 0.03 (31.35% of Total)
+| Total time 0.08 (100.0% of ALL )

 | Highest rstack allocated: 0
 | Highest istack allocated: 0
-| Job began at 17:24:36.294 on 12/10/2005
-| Setup done at 17:24:36.300 on 12/10/2005
-| Run done at 17:24:36.425 on 12/10/2005
+| Job began at 12:34:16.793 on 07/15/2009
+| Setup done at 12:34:16.813 on 07/15/2009
+| Run done at 12:34:16.877 on 07/15/2009
 | wallclock() was called 46 times
Index: test/pbsa_radi/out.save/da.out.save
===================================================================
--- test/pbsa_radi/out.save/da.out.save (original)
+++ test/pbsa_radi/out.save/da.out.save (working copy)
.@ -3,7 +3,7 @@
           Amber 9 PBSA Scripps/UCSF 2006
           -------------------------------------------------------

-| Run on 12/10/2005 at 17:24:36
+| Run on 07/15/2009 at 12:34:16
   [-O]verwriting output

 File Assignments:
.@ -31,11 +31,11 @@
    igb=10, ntb=0,
    ntc=1, ntf=1, tol=0.000001,
    ntt=0, temp0=300
- /
+ /
  &pb
    npbverb=0, epsout=80.0, radiopt=1, space=0.5,
    accept=1e-4, fillratio=6, sprob=1.6
- /
+ /

 ---------------------------------------------------------------------------
-----
    1. RESOURCE USE:
.@ -109,17 +109,17 @@

  Total surface charge 0.0000
  Reaction field energy -12.7277
- Cavity solvation energy 13.8221
- Dispersion solvation energy -15.6056
+ Cavity solvation energy 13.8065
+ Dispersion solvation energy -15.5853


    NSTEP ENERGY RMS GMAX NAME NUMBER
- 1 -9.5231E+01 5.1588E+00 1.8472E+01 N1 11
+ 1 -9.5227E+01 5.1587E+00 1.8470E+01 N1 11

  BOND = 0.0058 ANGLE = 0.0467 DIHED =
0.0062
  VDWAALS = -1.0176 EEL = -15.8966 EPB =
-12.7277
  1-4 VDW = 6.6808 1-4 EEL = -70.5454 RESTRAINT =
0.0000
- ECAVITY = 13.8221 EDISPER = -15.6056
+ ECAVITY = 13.8065 EDISPER = -15.5853


   Maximum number of minimization cycles reached.
.@ -130,44 +130,43 @@


    NSTEP ENERGY RMS GMAX NAME NUMBER
- 1 -9.5231E+01 5.1588E+00 1.8472E+01 N1 11
+ 1 -9.5227E+01 5.1587E+00 1.8470E+01 N1 11

  BOND = 0.0058 ANGLE = 0.0467 DIHED =
0.0062
  VDWAALS = -1.0176 EEL = -15.8966 EPB =
-12.7277
  1-4 VDW = 6.6808 1-4 EEL = -70.5454 RESTRAINT =
0.0000
- ECAVITY = 13.8221 EDISPER = -15.6056
+ ECAVITY = 13.8065 EDISPER = -15.5853

 ---------------------------------------------------------------------------
-----
    5. TIMINGS
 ---------------------------------------------------------------------------
-----

-| Read coords time 0.00 ( 0.23% of Total)
+| Read coords time 0.01 (18.82% of Total)
 | Fast Water setup 0.00 ( 0.02% of Total)
-| PB NB list 0.00 ( 0.05% of PB No)
-| PB FD grid 0.00 ( 2.55% of PB No)
-| PB Epsmap 0.01 (11.52% of PB FD)
-| PB Solver 0.07 (86.71% of PB FD)
-| Other 0.00 ( 1.77% of PB FD)
-| PB FD Force 0.08 (97.32% of PB No)
+| PB NB list 0.00 ( 0.06% of PB No)
+| PB FD grid 0.00 ( 3.48% of PB No)
+| PB Epsmap 0.01 (14.34% of PB FD)
+| PB Solver 0.03 (83.77% of PB FD)
+| Other 0.00 ( 1.89% of PB FD)
+| PB FD Force 0.04 (96.42% of PB No)
 | PB Direct 0.00 ( 0.03% of PB No)
-| Other 0.00 ( 0.04% of PB No)
-| PB Nonbond 0.09 (95.61% of Nonbo)
-| NP Sasa 0.00 (63.69% of NP No)
-| NP Cavity 0.00 ( 1.05% of NP No)
-| NP Dispersion 0.00 (34.65% of NP No)
-| Other 0.00 ( 0.60% of NP No)
-| NP Nonbond 0.00 ( 4.39% of Nonbo)
-| Nonbond force 0.09 (99.76% of Force)
-| Bond/Angle/Dihedral 0.00 ( 0.22% of Force)
-| Other 0.00 ( 0.02% of Force)
-| Force time 0.09 (100.0% of Runmd)
-| Runmd Time 0.09 (90.10% of Total)
-| Other 0.01 ( 9.65% of Total)
-| Total time 0.10 (100.0% of ALL )
+| Other 0.00 ( 0.01% of PB No)
+| PB Nonbond 0.04 (94.04% of Nonbo)
+| NP Sasa 0.00 (66.78% of NP No)
+| NP Cavity 0.00 ( 0.27% of NP No)
+| NP Dispersion 0.00 (32.94% of NP No)
+| NP Nonbond 0.00 ( 5.96% of Nonbo)
+| Nonbond force 0.04 (99.75% of Force)
+| Bond/Angle/Dihedral 0.00 ( 0.24% of Force)
+| Other 0.00 ( 0.01% of Force)
+| Force time 0.04 (100.0% of Runmd)
+| Runmd Time 0.04 (64.93% of Total)
+| Other 0.01 (16.24% of Total)
+| Total time 0.07 (100.0% of ALL )

 | Highest rstack allocated: 0
 | Highest istack allocated: 0
-| Job began at 17:24:36.474 on 12/10/2005
-| Setup done at 17:24:36.480 on 12/10/2005
-| Run done at 17:24:36.575 on 12/10/2005
+| Job began at 12:34:16.931 on 07/15/2009
+| Setup done at 12:34:16.950 on 07/15/2009
+| Run done at 12:34:16.998 on 07/15/2009
 | wallclock() was called 46 times
Index: test/pbsa_radi/out.save/hid.out.save
===================================================================
--- test/pbsa_radi/out.save/hid.out.save (original)
+++ test/pbsa_radi/out.save/hid.out.save (working copy)
.@ -3,7 +3,7 @@
           Amber 9 PBSA Scripps/UCSF 2006
           -------------------------------------------------------

-| Run on 12/10/2005 at 17:24:34
+| Run on 07/15/2009 at 12:34:15
   [-O]verwriting output

 File Assignments:
.@ -31,11 +31,11 @@
    igb=10, ntb=0,
    ntc=1, ntf=1, tol=0.000001,
    ntt=0, temp0=300
- /
+ /
  &pb
    npbverb=0, epsout=80.0, radiopt=1, space=0.5,
    accept=1e-4, fillratio=6, sprob=1.6
- /
+ /

 ---------------------------------------------------------------------------
-----
    1. RESOURCE USE:
.@ -109,17 +109,17 @@

  Total surface charge 0.0000
  Reaction field energy -9.0993
- Cavity solvation energy 10.9589
- Dispersion solvation energy -10.2628
+ Cavity solvation energy 10.9433
+ Dispersion solvation energy -10.2420


    NSTEP ENERGY RMS GMAX NAME NUMBER
- 1 4.7651E+00 2.3338E+00 8.8915E+00 ND1 5
+ 1 4.7704E+00 2.3339E+00 8.8918E+00 ND1 5

  BOND = 0.1008 ANGLE = 18.6106 DIHED =
0.0001
  VDWAALS = -0.1620 EEL = 6.2443 EPB =
-9.0993
  1-4 VDW = -0.0837 1-4 EEL = -11.5415 RESTRAINT =
0.0000
- ECAVITY = 10.9589 EDISPER = -10.2628
+ ECAVITY = 10.9433 EDISPER = -10.2420


   Maximum number of minimization cycles reached.
.@ -130,45 +130,44 @@


    NSTEP ENERGY RMS GMAX NAME NUMBER
- 1 4.7651E+00 2.3338E+00 8.8915E+00 ND1 5
+ 1 4.7704E+00 2.3339E+00 8.8918E+00 ND1 5

  BOND = 0.1008 ANGLE = 18.6106 DIHED =
0.0001
  VDWAALS = -0.1620 EEL = 6.2443 EPB =
-9.0993
  1-4 VDW = -0.0837 1-4 EEL = -11.5415 RESTRAINT =
0.0000
- ECAVITY = 10.9589 EDISPER = -10.2628
+ ECAVITY = 10.9433 EDISPER = -10.2420

 ---------------------------------------------------------------------------
-----
    5. TIMINGS
 ---------------------------------------------------------------------------
-----

-| Read coords time 0.00 ( 0.23% of Total)
-| Fast Water setup 0.00 ( 0.02% of Total)
+| Read coords time 0.00 ( 0.49% of Total)
+| Fast Water setup 0.00 ( 0.01% of Total)
 | PB NB list 0.00 ( 0.06% of PB No)
-| PB FD grid 0.00 ( 1.70% of PB No)
-| PB Epsmap 0.01 ( 8.61% of PB FD)
-| PB Solver 0.07 (90.41% of PB FD)
-| Other 0.00 ( 0.98% of PB FD)
-| PB FD Force 0.07 (98.17% of PB No)
-| PB Direct 0.00 ( 0.02% of PB No)
-| PB Multiple 0.00 ( 0.01% of PB No)
-| Other 0.00 ( 0.05% of PB No)
-| PB Nonbond 0.07 (97.08% of Nonbo)
-| NP Sasa 0.00 (63.40% of NP No)
-| NP Cavity 0.00 ( 1.33% of NP No)
-| NP Dispersion 0.00 (34.21% of NP No)
-| Other 0.00 ( 1.06% of NP No)
-| NP Nonbond 0.00 ( 2.92% of Nonbo)
-| Nonbond force 0.08 (99.75% of Force)
-| Bond/Angle/Dihedral 0.00 ( 0.23% of Force)
-| Other 0.00 ( 0.02% of Force)
-| Force time 0.08 (100.0% of Runmd)
-| Runmd Time 0.08 (84.43% of Total)
-| Other 0.01 (15.32% of Total)
-| Total time 0.09 (100.0% of ALL )
+| PB FD grid 0.00 ( 2.31% of PB No)
+| PB Epsmap 0.00 ( 9.71% of PB FD)
+| PB Solver 0.03 (89.21% of PB FD)
+| Other 0.00 ( 1.08% of PB FD)
+| PB FD Force 0.03 (97.60% of PB No)
+| PB Direct 0.00 ( 0.03% of PB No)
+| Other 0.00 ( 0.01% of PB No)
+| PB Nonbond 0.04 (96.07% of Nonbo)
+| NP Sasa 0.00 (67.41% of NP No)
+| NP Cavity 0.00 ( 0.48% of NP No)
+| NP Dispersion 0.00 (32.04% of NP No)
+| Other 0.00 ( 0.07% of NP No)
+| NP Nonbond 0.00 ( 3.93% of Nonbo)
+| Nonbond force 0.04 (99.74% of Force)
+| Bond/Angle/Dihedral 0.00 ( 0.25% of Force)
+| Other 0.00 ( 0.01% of Force)
+| Force time 0.04 (100.0% of Runmd)
+| Runmd Time 0.04 (61.13% of Total)
+| Other 0.02 (38.37% of Total)
+| Total time 0.06 (100.0% of ALL )

 | Highest rstack allocated: 0
 | Highest istack allocated: 0
-| Job began at 17:24:34.215 on 12/10/2005
-| Setup done at 17:24:34.221 on 12/10/2005
-| Run done at 17:24:34.306 on 12/10/2005
+| Job began at 12:34:15.105 on 07/15/2009
+| Setup done at 12:34:15.124 on 07/15/2009
+| Run done at 12:34:15.166 on 07/15/2009
 | wallclock() was called 46 times
Index: test/pbsa_radi/out.save/ru.out.save
===================================================================
--- test/pbsa_radi/out.save/ru.out.save (original)
+++ test/pbsa_radi/out.save/ru.out.save (working copy)
.@ -3,7 +3,7 @@
           Amber 9 PBSA Scripps/UCSF 2006
           -------------------------------------------------------

-| Run on 12/10/2005 at 17:24:37
+| Run on 07/15/2009 at 12:34:17
   [-O]verwriting output

 File Assignments:
.@ -31,11 +31,11 @@
    igb=10, ntb=0,
    ntc=1, ntf=1, tol=0.000001,
    ntt=0, temp0=300
- /
+ /
  &pb
    npbverb=0, epsout=80.0, radiopt=1, space=0.5,
    accept=1e-4, fillratio=6, sprob=1.6
- /
+ /

 ---------------------------------------------------------------------------
-----
    1. RESOURCE USE:
.@ -109,17 +109,17 @@

  Total surface charge 0.0000
  Reaction field energy -14.6310
- Cavity solvation energy 12.4603
- Dispersion solvation energy -13.4941
+ Cavity solvation energy 12.4440
+ Dispersion solvation energy -13.4794


    NSTEP ENERGY RMS GMAX NAME NUMBER
- 1 -8.0179E+01 4.6967E+00 1.8247E+01 O2 12
+ 1 -8.0181E+01 4.6967E+00 1.8247E+01 O2 12

  BOND = 0.0021 ANGLE = 0.0968 DIHED =
0.0062
  VDWAALS = 0.8304 EEL = 18.9134 EPB =
-14.6310
  1-4 VDW = 5.5961 1-4 EEL = -89.9597 RESTRAINT =
0.0000
- ECAVITY = 12.4603 EDISPER = -13.4941
+ ECAVITY = 12.4440 EDISPER = -13.4794


   Maximum number of minimization cycles reached.
.@ -130,45 +130,44 @@


    NSTEP ENERGY RMS GMAX NAME NUMBER
- 1 -8.0179E+01 4.6967E+00 1.8247E+01 O2 12
+ 1 -8.0181E+01 4.6967E+00 1.8247E+01 O2 12

  BOND = 0.0021 ANGLE = 0.0968 DIHED =
0.0062
  VDWAALS = 0.8304 EEL = 18.9134 EPB =
-14.6310
  1-4 VDW = 5.5961 1-4 EEL = -89.9597 RESTRAINT =
0.0000
- ECAVITY = 12.4603 EDISPER = -13.4941
+ ECAVITY = 12.4440 EDISPER = -13.4794

 ---------------------------------------------------------------------------
-----
    5. TIMINGS
 ---------------------------------------------------------------------------
-----

-| Read coords time 0.00 ( 0.26% of Total)
+| Read coords time 0.00 ( 0.61% of Total)
 | Fast Water setup 0.00 ( 0.02% of Total)
 | PB NB list 0.00 ( 0.06% of PB No)
-| PB FD grid 0.00 ( 2.36% of PB No)
-| PB Epsmap 0.01 (10.96% of PB FD)
-| PB Solver 0.07 (87.67% of PB FD)
-| Other 0.00 ( 1.37% of PB FD)
-| PB FD Force 0.07 (97.51% of PB No)
-| PB Direct 0.00 ( 0.02% of PB No)
-| PB Multiple 0.00 ( 0.01% of PB No)
-| Other 0.00 ( 0.05% of PB No)
-| PB Nonbond 0.08 (95.92% of Nonbo)
-| NP Sasa 0.00 (65.10% of NP No)
-| NP Cavity 0.00 ( 1.02% of NP No)
-| NP Dispersion 0.00 (33.14% of NP No)
-| Other 0.00 ( 0.74% of NP No)
-| NP Nonbond 0.00 ( 4.08% of Nonbo)
-| Nonbond force 0.08 (99.75% of Force)
-| Bond/Angle/Dihedral 0.00 ( 0.23% of Force)
-| Other 0.00 ( 0.02% of Force)
-| Force time 0.08 (100.0% of Runmd)
-| Runmd Time 0.08 (88.10% of Total)
-| Other 0.01 (11.62% of Total)
-| Total time 0.09 (99.90% of ALL )
+| PB FD grid 0.00 ( 3.25% of PB No)
+| PB Epsmap 0.00 (13.58% of PB FD)
+| PB Solver 0.03 (84.90% of PB FD)
+| Other 0.00 ( 1.52% of PB FD)
+| PB FD Force 0.03 (96.65% of PB No)
+| PB Direct 0.00 ( 0.03% of PB No)
+| Other 0.00 ( 0.01% of PB No)
+| PB Nonbond 0.04 (94.64% of Nonbo)
+| NP Sasa 0.00 (67.28% of NP No)
+| NP Cavity 0.00 ( 0.35% of NP No)
+| NP Dispersion 0.00 (32.28% of NP No)
+| Other 0.00 ( 0.10% of NP No)
+| NP Nonbond 0.00 ( 5.36% of Nonbo)
+| Nonbond force 0.04 (99.72% of Force)
+| Bond/Angle/Dihedral 0.00 ( 0.28% of Force)
+| Other 0.00 ( 0.01% of Force)
+| Force time 0.04 (100.0% of Runmd)
+| Runmd Time 0.04 (67.63% of Total)
+| Other 0.02 (31.75% of Total)
+| Total time 0.06 (100.0% of ALL )

 | Highest rstack allocated: 0
 | Highest istack allocated: 0
-| Job began at 17:24:37.068 on 12/10/2005
-| Setup done at 17:24:37.075 on 12/10/2005
-| Run done at 17:24:37.159 on 12/10/2005
+| Job began at 12:34:17.390 on 07/15/2009
+| Setup done at 12:34:17.401 on 07/15/2009
+| Run done at 12:34:17.446 on 07/15/2009
 | wallclock() was called 46 times
Index: test/pbsa_radi/out.save/ranp.out.save
===================================================================
--- test/pbsa_radi/out.save/ranp.out.save (original)
+++ test/pbsa_radi/out.save/ranp.out.save (working copy)
.@ -3,7 +3,7 @@
           Amber 9 PBSA Scripps/UCSF 2006
           -------------------------------------------------------

-| Run on 12/10/2005 at 17:24:39
+| Run on 07/15/2009 at 12:34:18
   [-O]verwriting output

 File Assignments:
.@ -31,11 +31,11 @@
    igb=10, ntb=0,
    ntc=1, ntf=1, tol=0.000001,
    ntt=0, temp0=300
- /
+ /
  &pb
    npbverb=0, epsout=80.0, radiopt=1, space=0.5,
    accept=1e-4, fillratio=6, sprob=1.6
- /
+ /

 ---------------------------------------------------------------------------
-----
    1. RESOURCE USE:
.@ -109,17 +109,17 @@

  Total surface charge 0.0000
  Reaction field energy -16.5711
- Cavity solvation energy 12.2265
- Dispersion solvation energy -13.2540
+ Cavity solvation energy 12.2001
+ Dispersion solvation energy -13.2176


    NSTEP ENERGY RMS GMAX NAME NUMBER
- 1 5.6230E+01 1.3847E+01 7.1036E+01 O5' 2
+ 1 5.6240E+01 1.3847E+01 7.1035E+01 O5' 2

  BOND = 0.0125 ANGLE = 2.4661 DIHED =
12.5170
  VDWAALS = 16.6286 EEL = -56.1863 EPB =
-16.5711
  1-4 VDW = 6.7100 1-4 EEL = 91.6803 RESTRAINT =
0.0000
- ECAVITY = 12.2265 EDISPER = -13.2540
+ ECAVITY = 12.2001 EDISPER = -13.2176


   Maximum number of minimization cycles reached.
.@ -130,44 +130,42 @@


    NSTEP ENERGY RMS GMAX NAME NUMBER
- 1 5.6230E+01 1.3847E+01 7.1036E+01 O5' 2
+ 1 5.6240E+01 1.3847E+01 7.1035E+01 O5' 2

  BOND = 0.0125 ANGLE = 2.4661 DIHED =
12.5170
  VDWAALS = 16.6286 EEL = -56.1863 EPB =
-16.5711
  1-4 VDW = 6.7100 1-4 EEL = 91.6803 RESTRAINT =
0.0000
- ECAVITY = 12.2265 EDISPER = -13.2540
+ ECAVITY = 12.2001 EDISPER = -13.2176

 ---------------------------------------------------------------------------
-----
    5. TIMINGS
 ---------------------------------------------------------------------------
-----

-| Read coords time 0.00 ( 0.23% of Total)
+| Read coords time 0.00 ( 0.62% of Total)
 | Fast Water setup 0.00 ( 0.02% of Total)
-| PB NB list 0.00 ( 0.05% of PB No)
-| PB FD grid 0.00 ( 2.18% of PB No)
-| PB Epsmap 0.01 (10.35% of PB FD)
-| PB Solver 0.07 (88.12% of PB FD)
-| Other 0.00 ( 1.53% of PB FD)
-| PB FD Force 0.08 (97.69% of PB No)
-| PB Direct 0.00 ( 0.03% of PB No)
-| Other 0.00 ( 0.05% of PB No)
-| PB Nonbond 0.08 (95.51% of Nonbo)
-| NP Sasa 0.00 (68.26% of NP No)
-| NP Cavity 0.00 ( 1.12% of NP No)
-| NP Dispersion 0.00 (29.99% of NP No)
-| Other 0.00 ( 0.63% of NP No)
-| NP Nonbond 0.00 ( 4.49% of Nonbo)
-| Nonbond force 0.09 (99.73% of Force)
-| Bond/Angle/Dihedral 0.00 ( 0.25% of Force)
-| Other 0.00 ( 0.02% of Force)
-| Force time 0.09 (100.0% of Runmd)
-| Runmd Time 0.09 (85.45% of Total)
-| Other 0.01 (14.30% of Total)
-| Total time 0.10 (100.0% of ALL )
+| PB NB list 0.00 ( 0.06% of PB No)
+| PB FD grid 0.00 ( 3.13% of PB No)
+| PB Epsmap 0.00 (12.98% of PB FD)
+| PB Solver 0.03 (85.30% of PB FD)
+| Other 0.00 ( 1.72% of PB FD)
+| PB FD Force 0.04 (96.76% of PB No)
+| PB Direct 0.00 ( 0.04% of PB No)
+| Other 0.00 ( 0.01% of PB No)
+| PB Nonbond 0.04 (93.90% of Nonbo)
+| NP Sasa 0.00 (70.19% of NP No)
+| NP Cavity 0.00 ( 0.33% of NP No)
+| NP Dispersion 0.00 (29.48% of NP No)
+| NP Nonbond 0.00 ( 6.10% of Nonbo)
+| Nonbond force 0.04 (99.71% of Force)
+| Bond/Angle/Dihedral 0.00 ( 0.28% of Force)
+| Force time 0.04 (100.0% of Runmd)
+| Runmd Time 0.04 (74.12% of Total)
+| Other 0.01 (25.25% of Total)
+| Total time 0.05 (100.0% of ALL )

 | Highest rstack allocated: 0
 | Highest istack allocated: 0
-| Job began at 17:24:39.058 on 12/10/2005
-| Setup done at 17:24:39.065 on 12/10/2005
-| Run done at 17:24:39.159 on 12/10/2005
+| Job began at 12:34:18.765 on 07/15/2009
+| Setup done at 12:34:18.772 on 07/15/2009
+| Run done at 12:34:18.819 on 07/15/2009
 | wallclock() was called 46 times
Index: test/pbsa_radi/out.save/hie.out.save
===================================================================
--- test/pbsa_radi/out.save/hie.out.save (original)
+++ test/pbsa_radi/out.save/hie.out.save (working copy)
.@ -3,7 +3,7 @@
           Amber 9 PBSA Scripps/UCSF 2006
           -------------------------------------------------------

-| Run on 12/10/2005 at 17:24:34
+| Run on 07/15/2009 at 12:34:15
   [-O]verwriting output

 File Assignments:
.@ -31,11 +31,11 @@
    igb=10, ntb=0,
    ntc=1, ntf=1, tol=0.000001,
    ntt=0, temp0=300
- /
+ /
  &pb
    npbverb=0, epsout=80.0, radiopt=1, space=0.5,
    accept=1e-4, fillratio=6, sprob=1.6
- /
+ /

 ---------------------------------------------------------------------------
-----
    1. RESOURCE USE:
.@ -109,17 +109,17 @@

  Total surface charge 0.0000
  Reaction field energy -9.4599
- Cavity solvation energy 11.0543
- Dispersion solvation energy -10.4107
+ Cavity solvation energy 11.0380
+ Dispersion solvation energy -10.3970


    NSTEP ENERGY RMS GMAX NAME NUMBER
- 1 5.3932E+00 2.2451E+00 5.9104E+00 HE2 9
+ 1 5.3907E+00 2.2451E+00 5.9104E+00 HE2 9

  BOND = 0.0768 ANGLE = 18.4254 DIHED =
0.0001
  VDWAALS = -0.1604 EEL = 3.3614 EPB =
-9.4599
  1-4 VDW = -0.0445 1-4 EEL = -7.4492 RESTRAINT =
0.0000
- ECAVITY = 11.0543 EDISPER = -10.4107
+ ECAVITY = 11.0380 EDISPER = -10.3970


   Maximum number of minimization cycles reached.
.@ -130,45 +130,42 @@


    NSTEP ENERGY RMS GMAX NAME NUMBER
- 1 5.3932E+00 2.2451E+00 5.9104E+00 HE2 9
+ 1 5.3907E+00 2.2451E+00 5.9104E+00 HE2 9

  BOND = 0.0768 ANGLE = 18.4254 DIHED =
0.0001
  VDWAALS = -0.1604 EEL = 3.3614 EPB =
-9.4599
  1-4 VDW = -0.0445 1-4 EEL = -7.4492 RESTRAINT =
0.0000
- ECAVITY = 11.0543 EDISPER = -10.4107
+ ECAVITY = 11.0380 EDISPER = -10.3970

 ---------------------------------------------------------------------------
-----
    5. TIMINGS
 ---------------------------------------------------------------------------
-----

-| Read coords time 0.00 ( 0.27% of Total)
+| Read coords time 0.00 ( 0.50% of Total)
 | Fast Water setup 0.00 ( 0.02% of Total)
 | PB NB list 0.00 ( 0.06% of PB No)
-| PB FD grid 0.00 ( 1.81% of PB No)
-| PB Epsmap 0.01 ( 9.23% of PB FD)
-| PB Solver 0.06 (89.67% of PB FD)
-| Other 0.00 ( 1.10% of PB FD)
-| PB FD Force 0.07 (98.05% of PB No)
-| PB Direct 0.00 ( 0.03% of PB No)
-| PB Multiple 0.00 ( 0.01% of PB No)
-| Other 0.00 ( 0.05% of PB No)
-| PB Nonbond 0.07 (96.88% of Nonbo)
-| NP Sasa 0.00 (62.48% of NP No)
-| NP Cavity 0.00 ( 1.14% of NP No)
-| NP Dispersion 0.00 (35.24% of NP No)
-| Other 0.00 ( 1.14% of NP No)
-| NP Nonbond 0.00 ( 3.12% of Nonbo)
-| Nonbond force 0.07 (99.71% of Force)
-| Bond/Angle/Dihedral 0.00 ( 0.26% of Force)
-| Other 0.00 ( 0.03% of Force)
-| Force time 0.07 (100.0% of Runmd)
-| Runmd Time 0.07 (83.63% of Total)
-| Other 0.01 (16.09% of Total)
-| Total time 0.08 (99.89% of ALL )
+| PB FD grid 0.00 ( 2.48% of PB No)
+| PB Epsmap 0.00 (11.83% of PB FD)
+| PB Solver 0.03 (87.00% of PB FD)
+| Other 0.00 ( 1.17% of PB FD)
+| PB FD Force 0.03 (97.43% of PB No)
+| PB Direct 0.00 ( 0.02% of PB No)
+| Other 0.00 ( 0.01% of PB No)
+| PB Nonbond 0.03 (95.89% of Nonbo)
+| NP Sasa 0.00 (66.71% of NP No)
+| NP Cavity 0.00 ( 0.56% of NP No)
+| NP Dispersion 0.00 (32.73% of NP No)
+| NP Nonbond 0.00 ( 4.11% of Nonbo)
+| Nonbond force 0.03 (99.73% of Force)
+| Bond/Angle/Dihedral 0.00 ( 0.27% of Force)
+| Force time 0.03 (100.0% of Runmd)
+| Runmd Time 0.03 (53.52% of Total)
+| Other 0.03 (45.96% of Total)
+| Total time 0.07 (100.0% of ALL )

 | Highest rstack allocated: 0
 | Highest istack allocated: 0
-| Job began at 17:24:34.355 on 12/10/2005
-| Setup done at 17:24:34.361 on 12/10/2005
-| Run done at 17:24:34.439 on 12/10/2005
+| Job began at 12:34:15.213 on 07/15/2009
+| Setup done at 12:34:15.237 on 07/15/2009
+| Run done at 12:34:15.278 on 07/15/2009
 | wallclock() was called 46 times
Index: test/pbsa_radi/out.save/dt.out.save
===================================================================
--- test/pbsa_radi/out.save/dt.out.save (original)
+++ test/pbsa_radi/out.save/dt.out.save (working copy)
.@ -3,7 +3,7 @@
           Amber 9 PBSA Scripps/UCSF 2006
           -------------------------------------------------------

-| Run on 12/10/2005 at 17:24:36
+| Run on 07/15/2009 at 12:34:17
   [-O]verwriting output

 File Assignments:
.@ -31,11 +31,11 @@
    igb=10, ntb=0,
    ntc=1, ntf=1, tol=0.000001,
    ntt=0, temp0=300
- /
+ /
  &pb
    npbverb=0, epsout=80.0, radiopt=1, space=0.5,
    accept=1e-4, fillratio=6, sprob=1.6
- /
+ /

 ---------------------------------------------------------------------------
-----
    1. RESOURCE USE:
.@ -109,17 +109,17 @@

  Total surface charge 0.0000
  Reaction field energy -14.5124
- Cavity solvation energy 13.9056
- Dispersion solvation energy -14.6078
+ Cavity solvation energy 13.8914
+ Dispersion solvation energy -14.5874


    NSTEP ENERGY RMS GMAX NAME NUMBER
- 1 -4.9762E+01 4.9889E+00 1.9025E+01 O2 15
+ 1 -4.9756E+01 4.9889E+00 1.9025E+01 O2 15

  BOND = 0.0024 ANGLE = 0.1078 DIHED =
5.7144
  VDWAALS = 1.0665 EEL = -24.4256 EPB =
-14.5124
  1-4 VDW = 6.3577 1-4 EEL = -23.3709 RESTRAINT =
0.0000
- ECAVITY = 13.9056 EDISPER = -14.6078
+ ECAVITY = 13.8914 EDISPER = -14.5874


   Maximum number of minimization cycles reached.
.@ -130,44 +130,43 @@


    NSTEP ENERGY RMS GMAX NAME NUMBER
- 1 -4.9762E+01 4.9889E+00 1.9025E+01 O2 15
+ 1 -4.9756E+01 4.9889E+00 1.9025E+01 O2 15

  BOND = 0.0024 ANGLE = 0.1078 DIHED =
5.7144
  VDWAALS = 1.0665 EEL = -24.4256 EPB =
-14.5124
  1-4 VDW = 6.3577 1-4 EEL = -23.3709 RESTRAINT =
0.0000
- ECAVITY = 13.9056 EDISPER = -14.6078
+ ECAVITY = 13.8914 EDISPER = -14.5874

 ---------------------------------------------------------------------------
-----
    5. TIMINGS
 ---------------------------------------------------------------------------
-----

-| Read coords time 0.00 ( 0.22% of Total)
+| Read coords time 0.00 ( 0.63% of Total)
 | Fast Water setup 0.00 ( 0.02% of Total)
-| PB NB list 0.00 ( 0.05% of PB No)
-| PB FD grid 0.00 ( 2.21% of PB No)
-| PB Epsmap 0.01 (10.25% of PB FD)
-| PB Solver 0.08 (88.28% of PB FD)
-| Other 0.00 ( 1.47% of PB FD)
-| PB FD Force 0.09 (97.68% of PB No)
+| PB NB list 0.00 ( 0.06% of PB No)
+| PB FD grid 0.00 ( 3.05% of PB No)
+| PB Epsmap 0.01 (12.84% of PB FD)
+| PB Solver 0.03 (85.46% of PB FD)
+| Other 0.00 ( 1.70% of PB FD)
+| PB FD Force 0.04 (96.85% of PB No)
 | PB Direct 0.00 ( 0.03% of PB No)
-| Other 0.00 ( 0.04% of PB No)
-| PB Nonbond 0.09 (95.64% of Nonbo)
-| NP Sasa 0.00 (64.21% of NP No)
-| NP Cavity 0.00 ( 0.86% of NP No)
-| NP Dispersion 0.00 (34.35% of NP No)
-| Other 0.00 ( 0.58% of NP No)
-| NP Nonbond 0.00 ( 4.36% of Nonbo)
-| Nonbond force 0.10 (99.78% of Force)
-| Bond/Angle/Dihedral 0.00 ( 0.19% of Force)
-| Other 0.00 ( 0.02% of Force)
-| Force time 0.10 (100.0% of Runmd)
-| Runmd Time 0.10 (90.21% of Total)
-| Other 0.01 ( 9.56% of Total)
-| Total time 0.11 (100.0% of ALL )
+| Other 0.00 ( 0.01% of PB No)
+| PB Nonbond 0.04 (94.01% of Nonbo)
+| NP Sasa 0.00 (66.98% of NP No)
+| NP Cavity 0.00 ( 0.30% of NP No)
+| NP Dispersion 0.00 (32.69% of NP No)
+| Other 0.00 ( 0.04% of NP No)
+| NP Nonbond 0.00 ( 5.99% of Nonbo)
+| Nonbond force 0.04 (99.63% of Force)
+| Bond/Angle/Dihedral 0.00 ( 0.36% of Force)
+| Force time 0.04 (100.0% of Runmd)
+| Runmd Time 0.04 (77.66% of Total)
+| Other 0.01 (21.70% of Total)
+| Total time 0.06 (100.0% of ALL )

 | Highest rstack allocated: 0
 | Highest istack allocated: 0
-| Job began at 17:24:36.914 on 12/10/2005
-| Setup done at 17:24:36.919 on 12/10/2005
-| Run done at 17:24:37.020 on 12/10/2005
+| Job began at 12:34:17.276 on 07/15/2009
+| Setup done at 12:34:17.282 on 07/15/2009
+| Run done at 12:34:17.334 on 07/15/2009
 | wallclock() was called 46 times
Index: test/pbsa_radi/out.save/alabk.out.save
===================================================================
--- test/pbsa_radi/out.save/alabk.out.save (original)
+++ test/pbsa_radi/out.save/alabk.out.save (working copy)
.@ -3,7 +3,7 @@
           Amber 9 PBSA Scripps/UCSF 2006
           -------------------------------------------------------

-| Run on 12/10/2005 at 17:24:35
+| Run on 07/15/2009 at 12:34:16
   [-O]verwriting output

 File Assignments:
.@ -31,11 +31,11 @@
    igb=10, ntb=0,
    ntc=1, ntf=1, tol=0.000001,
    ntt=0, temp0=300
- /
+ /
  &pb
    npbverb=0, epsout=80.0, radiopt=1, space=0.5,
    accept=1e-4, fillratio=6, sprob=1.6
- /
+ /

 ---------------------------------------------------------------------------
-----
    1. RESOURCE USE:
.@ -109,17 +109,17 @@

  Total surface charge 0.0000
  Reaction field energy -13.5389
- Cavity solvation energy 15.9211
- Dispersion solvation energy -14.8102
+ Cavity solvation energy 15.9083
+ Dispersion solvation energy -14.7996


    NSTEP ENERGY RMS GMAX NAME NUMBER
- 1 -2.9899E+01 4.8948E+00 2.3427E+01 N 7
+ 1 -2.9901E+01 4.8948E+00 2.3427E+01 N 7

  BOND = 0.0005 ANGLE = 0.0453 DIHED =
7.9848
  VDWAALS = 1.0234 EEL = -80.9632 EPB =
-13.5389
  1-4 VDW = 5.0568 1-4 EEL = 49.3817 RESTRAINT =
0.0000
- ECAVITY = 15.9211 EDISPER = -14.8102
+ ECAVITY = 15.9083 EDISPER = -14.7996


   Maximum number of minimization cycles reached.
.@ -130,44 +130,43 @@


    NSTEP ENERGY RMS GMAX NAME NUMBER
- 1 -2.9899E+01 4.8948E+00 2.3427E+01 N 7
+ 1 -2.9901E+01 4.8948E+00 2.3427E+01 N 7

  BOND = 0.0005 ANGLE = 0.0453 DIHED =
7.9848
  VDWAALS = 1.0234 EEL = -80.9632 EPB =
-13.5389
  1-4 VDW = 5.0568 1-4 EEL = 49.3817 RESTRAINT =
0.0000
- ECAVITY = 15.9211 EDISPER = -14.8102
+ ECAVITY = 15.9083 EDISPER = -14.7996

 ---------------------------------------------------------------------------
-----
    5. TIMINGS
 ---------------------------------------------------------------------------
-----

-| Read coords time 0.00 ( 0.25% of Total)
-| Fast Water setup 0.00 ( 0.02% of Total)
-| PB NB list 0.00 ( 0.05% of PB No)
-| PB FD grid 0.00 ( 2.13% of PB No)
-| PB Epsmap 0.01 (10.53% of PB FD)
-| PB Solver 0.08 (87.70% of PB FD)
-| Other 0.00 ( 1.78% of PB FD)
-| PB FD Force 0.10 (97.75% of PB No)
-| PB Direct 0.00 ( 0.03% of PB No)
-| Other 0.00 ( 0.04% of PB No)
-| PB Nonbond 0.10 (94.34% of Nonbo)
-| NP Sasa 0.00 (64.22% of NP No)
-| NP Cavity 0.00 ( 0.71% of NP No)
-| NP Dispersion 0.00 (34.65% of NP No)
-| Other 0.00 ( 0.42% of NP No)
-| NP Nonbond 0.01 ( 5.66% of Nonbo)
-| Nonbond force 0.10 (99.77% of Force)
-| Bond/Angle/Dihedral 0.00 ( 0.21% of Force)
-| Other 0.00 ( 0.02% of Force)
-| Force time 0.10 (100.0% of Runmd)
-| Runmd Time 0.10 (91.17% of Total)
-| Other 0.01 ( 8.57% of Total)
-| Total time 0.11 (100.0% of ALL )
+| Read coords time 0.00 ( 0.49% of Total)
+| Fast Water setup 0.00 ( 0.01% of Total)
+| PB NB list 0.00 ( 0.06% of PB No)
+| PB FD grid 0.00 ( 3.20% of PB No)
+| PB Epsmap 0.01 (13.14% of PB FD)
+| PB Solver 0.04 (84.81% of PB FD)
+| Other 0.00 ( 2.05% of PB FD)
+| PB FD Force 0.04 (96.70% of PB No)
+| PB Direct 0.00 ( 0.04% of PB No)
+| Other 0.00 ( 0.01% of PB No)
+| PB Nonbond 0.04 (92.35% of Nonbo)
+| NP Sasa 0.00 (65.89% of NP No)
+| NP Cavity 0.00 ( 0.22% of NP No)
+| NP Dispersion 0.00 (33.87% of NP No)
+| Other 0.00 ( 0.03% of NP No)
+| NP Nonbond 0.00 ( 7.65% of Nonbo)
+| Nonbond force 0.05 (99.77% of Force)
+| Bond/Angle/Dihedral 0.00 ( 0.22% of Force)
+| Force time 0.05 (100.0% of Runmd)
+| Runmd Time 0.05 (69.87% of Total)
+| Other 0.02 (29.63% of Total)
+| Total time 0.07 (100.0% of ALL )

 | Highest rstack allocated: 0
 | Highest istack allocated: 0
-| Job began at 17:24:35.984 on 12/10/2005
-| Setup done at 17:24:35.990 on 12/10/2005
-| Run done at 17:24:36.099 on 12/10/2005
+| Job began at 12:34:16.587 on 07/15/2009
+| Setup done at 12:34:16.601 on 07/15/2009
+| Run done at 12:34:16.656 on 07/15/2009
 | wallclock() was called 46 times
Index: test/pbsa_trx/mdout.trxox.min.save
===================================================================
--- test/pbsa_trx/mdout.trxox.min.save (original)
+++ test/pbsa_trx/mdout.trxox.min.save (working copy)
.@ -3,7 +3,7 @@
           Amber 9 PBSA Scripps/UCSF 2006
           -------------------------------------------------------

-| Run on 12/10/2005 at 17:48:49
+| Run on 07/15/2009 at 12:34:05
   [-O]verwriting output

 File Assignments:
.@ -107,17 +107,17 @@

  Total surface charge 3.9725
  Reaction field energy -1791.1799
- Cavity solvation energy 273.9283
- Dispersion solvation energy -355.2636
+ Cavity solvation energy 273.8256
+ Dispersion solvation energy -355.1258


    NSTEP ENERGY RMS GMAX NAME NUMBER
- 1 -3.4556E+03 2.2314E+01 1.2198E+02 CA 1102
+ 1 -3.4555E+03 2.2314E+01 1.2198E+02 CA 1102

  BOND = 631.8993 ANGLE = 898.2543 DIHED =
566.4453
  VDWAALS = -730.6029 EEL = -9278.3669 EPB =
-1791.1799
  1-4 VDW = 348.8246 1-4 EEL = 5980.5047 RESTRAINT =
0.0000
- ECAVITY = 273.9283 EDISPER = -355.2636
+ ECAVITY = 273.8256 EDISPER = -355.1258


   Maximum number of minimization cycles reached.
.@ -128,39 +128,39 @@


    NSTEP ENERGY RMS GMAX NAME NUMBER
- 1 -3.4556E+03 2.2314E+01 1.2198E+02 CA 1102
+ 1 -3.4555E+03 2.2314E+01 1.2198E+02 CA 1102

  BOND = 631.8993 ANGLE = 898.2543 DIHED =
566.4453
  VDWAALS = -730.6029 EEL = -9278.3669 EPB =
-1791.1799
  1-4 VDW = 348.8246 1-4 EEL = 5980.5047 RESTRAINT =
0.0000
- ECAVITY = 273.9283 EDISPER = -355.2636
+ ECAVITY = 273.8256 EDISPER = -355.1258

 ---------------------------------------------------------------------------
-----
    5. TIMINGS
 ---------------------------------------------------------------------------
-----

-| Read coords time 0.01 ( 0.06% of Total)
-| PB NB list 0.08 ( 0.62% of PB No)
-| PB FD grid 0.71 ( 5.76% of PB No)
-| PB Epsmap 0.87 ( 7.55% of PB FD)
-| PB Solver 5.79 (50.02% of PB FD)
-| Other 4.91 (42.43% of PB FD)
-| PB FD Force 11.57 (93.51% of PB No)
-| PB Direct 0.01 ( 0.12% of PB No)
-| PB Nonbond 12.38 (83.57% of Nonbo)
-| NP Sasa 1.61 (66.02% of NP No)
-| NP Dispersion 0.83 (33.97% of NP No)
-| NP Nonbond 2.43 (16.43% of Nonbo)
-| Nonbond force 14.81 (100.0% of Force)
-| Bond/Angle/Dihedral 0.01 ( 0.06% of Force)
-| Force time 14.82 (100.0% of Runmd)
-| Runmd Time 14.82 (99.06% of Total)
-| Other 0.13 ( 0.88% of Total)
-| Total time 14.96 (100.0% of ALL )
+| Read coords time 0.03 ( 0.58% of Total)
+| PB NB list 0.02 ( 0.59% of PB No)
+| PB FD grid 0.26 ( 6.15% of PB No)
+| PB Epsmap 0.30 ( 7.73% of PB FD)
+| PB Solver 2.20 (56.67% of PB FD)
+| Other 1.38 (35.60% of PB FD)
+| PB FD Force 3.89 (93.16% of PB No)
+| PB Direct 0.00 ( 0.10% of PB No)
+| PB Nonbond 4.17 (84.41% of Nonbo)
+| NP Sasa 0.51 (65.94% of NP No)
+| NP Dispersion 0.26 (34.05% of NP No)
+| NP Nonbond 0.77 (15.59% of Nonbo)
+| Nonbond force 4.94 (100.0% of Force)
+| Bond/Angle/Dihedral 0.00 ( 0.04% of Force)
+| Force time 4.95 (100.0% of Runmd)
+| Runmd Time 4.95 (97.28% of Total)
+| Other 0.11 ( 2.14% of Total)
+| Total time 5.09 (100.0% of ALL )

 | Highest rstack allocated: 0
 | Highest istack allocated: 0
-| Job began at 17:48:49.933 on 12/10/2005
-| Setup done at 17:48:50.049 on 12/10/2005
-| Run done at 17:49:04.893 on 12/10/2005
+| Job began at 12:34:05.500 on 07/15/2009
+| Setup done at 12:34:05.611 on 07/15/2009
+| Run done at 12:34:10.585 on 07/15/2009
 | wallclock() was called 46 times
Index: test/pbsa_tsr/mdout.tsrb.min.save
===================================================================
--- test/pbsa_tsr/mdout.tsrb.min.save (original)
+++ test/pbsa_tsr/mdout.tsrb.min.save (working copy)
.@ -3,7 +3,7 @@
           Amber 9 PBSA Scripps/UCSF 2006
           -------------------------------------------------------

-| Run on 12/10/2005 at 17:49:43
+| Run on 07/15/2009 at 12:34:18
   [-O]verwriting output

 File Assignments:
.@ -107,17 +107,17 @@

  Total surface charge -2.9556
  Reaction field energy -2210.9292
- Cavity solvation energy 426.2063
- Dispersion solvation energy -597.9194
+ Cavity solvation energy 426.0937
+ Dispersion solvation energy -597.7718


    NSTEP ENERGY RMS GMAX NAME NUMBER
- 1 -7.5740E+03 2.8519E+00 2.0717E+01 OE2 2974
+ 1 -7.5739E+03 2.8519E+00 2.0717E+01 OE2 2974

  BOND = 110.0926 ANGLE = 415.3938 DIHED =
399.1931
  VDWAALS = -1534.2541 EEL = -10443.8159 EPB =
-2210.9292
  1-4 VDW = 496.0812 1-4 EEL = 5365.9913 RESTRAINT =
0.0000
- ECAVITY = 426.2063 EDISPER = -597.9194
+ ECAVITY = 426.0937 EDISPER = -597.7718


   Maximum number of minimization cycles reached.
.@ -128,39 +128,39 @@


    NSTEP ENERGY RMS GMAX NAME NUMBER
- 1 -7.5740E+03 2.8519E+00 2.0717E+01 OE2 2974
+ 1 -7.5739E+03 2.8519E+00 2.0717E+01 OE2 2974

  BOND = 110.0926 ANGLE = 415.3938 DIHED =
399.1931
  VDWAALS = -1534.2541 EEL = -10443.8159 EPB =
-2210.9292
  1-4 VDW = 496.0812 1-4 EEL = 5365.9913 RESTRAINT =
0.0000
- ECAVITY = 426.2063 EDISPER = -597.9194
+ ECAVITY = 426.0937 EDISPER = -597.7718

 ---------------------------------------------------------------------------
-----
    5. TIMINGS
 ---------------------------------------------------------------------------
-----

-| Read coords time 0.02 ( 0.17% of Total)
-| PB NB list 0.17 ( 3.00% of PB No)
-| PB FD grid 0.86 (14.87% of PB No)
-| PB Epsmap 0.21 ( 4.45% of PB FD)
-| PB Solver 0.95 (20.24% of PB FD)
-| Other 3.54 (75.31% of PB FD)
-| PB FD Force 4.69 (81.61% of PB No)
-| PB Direct 0.03 ( 0.51% of PB No)
-| PB Nonbond 5.75 (62.96% of Nonbo)
-| NP Sasa 1.76 (51.90% of NP No)
-| NP Dispersion 1.63 (48.10% of NP No)
-| NP Nonbond 3.38 (37.04% of Nonbo)
-| Nonbond force 9.14 (99.85% of Force)
-| Bond/Angle/Dihedral 0.01 ( 0.15% of Force)
-| Force time 9.15 (100.0% of Runmd)
-| Runmd Time 9.15 (97.88% of Total)
-| Other 0.18 ( 1.94% of Total)
-| Total time 9.35 (100.0% of ALL )
+| Read coords time 0.02 ( 0.74% of Total)
+| PB NB list 0.05 ( 3.09% of PB No)
+| PB FD grid 0.31 (17.33% of PB No)
+| PB Epsmap 0.07 ( 4.81% of PB FD)
+| PB Solver 0.37 (26.25% of PB FD)
+| Other 0.97 (68.94% of PB FD)
+| PB FD Force 1.40 (79.07% of PB No)
+| PB Direct 0.01 ( 0.50% of PB No)
+| PB Nonbond 1.77 (62.03% of Nonbo)
+| NP Sasa 0.61 (56.60% of NP No)
+| NP Dispersion 0.47 (43.40% of NP No)
+| NP Nonbond 1.08 (37.97% of Nonbo)
+| Nonbond force 2.86 (99.89% of Force)
+| Bond/Angle/Dihedral 0.00 ( 0.11% of Force)
+| Force time 2.86 (100.0% of Runmd)
+| Runmd Time 2.86 (95.84% of Total)
+| Other 0.10 ( 3.42% of Total)
+| Total time 2.98 (100.0% of ALL )

 | Highest rstack allocated: 0
 | Highest istack allocated: 0
-| Job began at 17:49:43.346 on 12/10/2005
-| Setup done at 17:49:43.506 on 12/10/2005
-| Run done at 17:49:52.695 on 12/10/2005
+| Job began at 12:34:18.887 on 07/15/2009
+| Setup done at 12:34:18.995 on 07/15/2009
+| Run done at 12:34:21.871 on 07/15/2009
 | wallclock() was called 46 times
----------------------------------------------------------------------------
Temporary workarounds: None



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Received on Thu Jul 16 2009 - 01:08:48 PDT
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