Hi,
I have been looking into geometry optimizations with sander using xmin
(ntmin=3) and sqm (which uses xmin by default). There are two problems
with the output and the testjobs for sander and sqm fail. This affects
both the Amber11 development tree (sander and sqm) and the AmberTools
1.3 release candidate (sqm).
I am running opensuse 11.2:
uname -a
Linux gecko 2.6.31.5-0.1-default #1 SMP 2009-10-26 15:49:03 +0100
x86_64 x86_64 x86_64 GNU/Linux
I compiled with Intel 11.0.074 with MKL:
ifort -V
Intel(R) C Intel(R) 64 Compiler Professional for applications running
on Intel(R) 64, Version 11.0 Build 20081105 Package ID:
l_cproc_p_11.0.074
and gnu compilers without MKL:
gcc --version
gcc (SUSE Linux) 4.4.1 [gcc-4_4-branch revision 150839]
Ross confirmed problems described below for Amber11 with Intel
Compiler version 10.1.018 on RHEL 5.
A) sander:
==========
Amber11 cvs tree (updated Dec 3rd, 2pm)
$AMBERHOME/test/dhfr/Run.dhfr.lmodxmin
--------------------------------------
I am attaching my output file (intel compiler) for reference
(mdout.dhfr.lmodxmin)
There are three issues:
1)
The RMS value of the gradient is printed as being zero for all steps
of the geometry optimization. The relevant code is in subroutine
run_xmin ($AMBERHOME/src/sander/lmod.f). The RMS value should be
returned by function xminc (variable grms), so something goes wrong
here - any help is appreciated.
In addition, for printing during the geometry optimization, this is
the *wrong place* to calculate the RMS value of the gradient. The
gradient is calculated in subroutine gradient_calc *after* call of
xminc and the progress of the minimization is printed after the
gradient has been calculated there by subroutine
report_min_progress. Thus either report_min_progress has to be called
outside of gradient_calc or the RMS of the gradient has to be
calculated in gradient_calc. Comments?
2)
The second error is that the number of steps NSTEP printed for the
FINAL RESULTS is wrong. The reason is that the variable xmin_iter (see
subroutine run_xmin in $AMBERHOME/src/sander/lmod.f) does not count
the number of iterations correctly. xmin_iter is updated by function
xminc - any idea what it counts? The variable n_force_calls contains
the correct number of geometry optimization steps (one force call per
geometry optimization step) and should probably be used instead. Comments?
3)
The geometry optimizer takes different steps. The energies and maximum
gradient element differ already after the first step.
I will file a bug report on the Amber Bugzilla about this.
According to the cvs log, the test
$AMBERHOME/test/dhfr/Run.dhfr.lmodxmin has been created only very
recently (2009/08/18). I checked the Amber10 manual and the xmin
method for geometry optimization is described there, so there should
be other test jobs to verify the implementation. I found only one
($AMBERHOME/test/gbrna/Run.gbrna.xmin) but it is not invoked by the
test Makefiles - any idea why? If invoked, this test fails for the
same reasons as given above.
B) sqm:
=======
AmberTools 1.3 RC (AmberTools.24nov09.tar.bz2):
AmberTools cvs tree (updated Dec 3rd, 2pm)
$AMBERHOME/test/antechamber/sustiva
-----------------------------------
I am attaching my output files (intel compiler) for reference
(sustiva.mol2 and sqm.out)
Charges in mol2 file are different (sustiva.mol2 vs sustiva.mol2.save).
Reason: sqm needs 105 additional geometry optimization steps to
converge and the energies are different already during the first
couple of steps. As a consequence the geometry and charges are
different. My guess is that this is related to the problems I observed
for sander since sqm is using xmin for geometry optimization.
I also compared the structures obtained from sqm with mopac (test
output in Amber10) - the structures (and obtained charges) are
different. I find this worrisome. Also, sqm requires many more steps
to converge the geometry than mopac does - this, however, may be
related to the coordinate set (Cartesian vs internal or redundant
internal?) in which the optimization is performed. I will set up
different test cases and look into this.
$AMBERHOME/test/antechamber/ash
-------------------------------
Charges in mol2 file are different (ash.mol2 vs ash.mol2.save).
Reason: Probably same as for $AMBERHOME/test/antechamber/sustiva (no
sqm.out.save here to check)
All other antechamber tests which use sqm for charge generation
pass. My guess is that the problem remains but the optimized
geometries are close enough to generate identical charges (there is no
way to check because there is no sqm.out.save).
$AMBERHOME/test/sqm/AM1
-----------------------
This test is not invoked by "make -f Makefile_at test" (is this
intentional?).
However, it fails when invoked manually. Again, the energies of the
geometry optimization steps are different and an additional 23 steps
are required for convergence which results in different geometry and
charges.
Thanks for your help and all the best,
Andy
--
Dr. Andreas W. Goetz
San Diego Supercomputer Center
Tel : +1-858-822-4771
Email: agoetz.sdsc.edu
Web : www.awgoetz.de
-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| Run on 12/03/2009 at 15:23:07
[-O]verwriting output
File Assignments:
| MDIN: gbin
| MDOUT: mdout.dhfr.lmodxmin
|INPCRD: md12.x
| PARM: prmtop
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
Here is the input file:
short lmod xmin minimization
&cntrl
ntx=7, irest=1,
ntc=2, ntf=2, tol=0.0000001,
imin=1, maxcyc=20,
ntpr=1, ntwr=10000,
ntmin = 3,
/
&lmod
xmin_verbosity = 1,
/
&ewald
nfft1 = 72, nfft2 = 60, nfft3 = 54,
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 27.261
| INFO: Old style PARM file read
NATOM = 22930 NTYPES = 17 NBONH = 21651 MBONA = 1302
NTHETH = 2789 MTHETA = 1772 NPHIH = 5026 MPHIA = 3140
NHPARM = 0 NPARM = 0 NNB = 41018 NRES = 6980
NBONA = 1302 NTHETA = 1772 NPHIA = 3140 NUMBND = 45
NUMANG = 91 NPTRA = 33 NATYP = 32 NPHB = 1
IFBOX = 1 NMXRS = 25 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 1461073
| Hollerith 75772
| Integer 931616
| Max Pairs 7643333
| nblistReal 275160
| nblist Int 1106696
| Total 51679 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 7, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 10000
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 1, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 20, ncyc = 10, ntmin = 3
dx0 = 0.01000, drms = 0.00010
LMOD:
xmin_method = LBFGS
lbfgs_memory_depth = 3
matrix_vector_product_method = forward finite difference
xmin_verbosity = 1
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 0
Box X = 70.063 Box Y = 60.543 Box Z = 54.523
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 72 NFFT2 = 60 NFFT3 = 54
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 510.050 ps
Number of triangulated 3-point waters found: 6810
Sum of charges from parm topology file = -0.00000006
Forcing neutrality...
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
LMOD XMIN Minimization.
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 4721242
| TOTAL SIZE OF NONBOND LIST = 4721242
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -7.1862E+04 0.0000E+00 1.0607E+02 C 1855
BOND = 452.1690 ANGLE = 1277.0334 DIHED = 968.3542
VDWAALS = 8109.3892 EEL = -89881.6441 HBOND = 0.0000
1-4 VDW = 545.9440 1-4 EEL = 6666.3920 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2 -9.2912E+04 0.0000E+00 5.2385E+02 C 1855
BOND = 3247.1617 ANGLE = 1447.8314 DIHED = 878.5948
VDWAALS = 6847.6223 EEL = -112512.6354 HBOND = 0.0000
1-4 VDW = 525.7464 1-4 EEL = 6653.8527 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
3 -1.2143E+05 0.0000E+00 1.8244E+02 CD 2092
BOND = 777.0478 ANGLE = 1012.5834 DIHED = 882.8657
VDWAALS = 6293.9572 EEL = -137549.8484 HBOND = 0.0000
1-4 VDW = 504.6835 1-4 EEL = 6652.5808 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
4 -1.5285E+05 0.0000E+00 4.7067E+02 CD 2092
BOND = 1501.5583 ANGLE = 944.2675 DIHED = 849.3082
VDWAALS = 6332.2217 EEL = -169652.5221 HBOND = 0.0000
1-4 VDW = 499.8234 1-4 EEL = 6672.4586 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
5 -2.1551E+05 0.0000E+00 8.1059E+02 CD 2092
BOND = 8810.0791 ANGLE = 3192.5878 DIHED = 934.9011
VDWAALS = 6410.6647 EEL = -242081.8203 HBOND = 0.0000
1-4 VDW = 527.9690 1-4 EEL = 6691.3683 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
6 -2.1551E+05 0.0000E+00 8.1059E+02 CD 2092
BOND = 8810.0791 ANGLE = 3192.5878 DIHED = 934.9011
VDWAALS = 6410.6647 EEL = -242081.8203 HBOND = 0.0000
1-4 VDW = 527.9690 1-4 EEL = 6691.3683 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
7 -2.4829E+05 0.0000E+00 1.3369E+03 O 22511
BOND = 24496.3152 ANGLE = 7749.0856 DIHED = 1140.9582
VDWAALS = 6969.3970 EEL = -295965.8149 HBOND = 0.0000
1-4 VDW = 611.8232 1-4 EEL = 6713.0850 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
8 -2.7612E+05 0.0000E+00 6.9152E+02 CG 2053
BOND = 10476.5922 ANGLE = 4024.7887 DIHED = 1017.2003
VDWAALS = 6835.5787 EEL = -305715.2521 HBOND = 0.0000
1-4 VDW = 543.3945 1-4 EEL = 6693.8194 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
9 -3.0831E+05 0.0000E+00 4.3283E+02 O 5624
BOND = 1779.8357 ANGLE = 1363.8115 DIHED = 909.8010
VDWAALS = 6996.1001 EEL = -326528.7374 HBOND = 0.0000
1-4 VDW = 496.8790 1-4 EEL = 6675.1139 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
10 -4.0606E+05 0.0000E+00 2.8879E+03 O 5624
BOND = 1795.5208 ANGLE = 1585.2717 DIHED = 977.6381
VDWAALS = 8066.1265 EEL = -425663.6581 HBOND = 0.0000
1-4 VDW = 504.1962 1-4 EEL = 6670.2204 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
11 -4.0606E+05 0.0000E+00 2.8879E+03 O 5624
BOND = 1795.5208 ANGLE = 1585.2717 DIHED = 977.6381
VDWAALS = 8066.1265 EEL = -425663.6581 HBOND = 0.0000
1-4 VDW = 504.1962 1-4 EEL = 6670.2204 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
12 -4.1905E+05 0.0000E+00 5.8477E+03 H1 15255
BOND = 1366.9082 ANGLE = 1435.8299 DIHED = 964.2067
VDWAALS = 8179.7089 EEL = -438167.7002 HBOND = 0.0000
1-4 VDW = 500.9903 1-4 EEL = 6668.0441 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
13 -4.1905E+05 0.0000E+00 5.8477E+03 H1 15255
BOND = 1366.9082 ANGLE = 1435.8299 DIHED = 964.2067
VDWAALS = 8179.7089 EEL = -438167.7002 HBOND = 0.0000
1-4 VDW = 500.9903 1-4 EEL = 6668.0441 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
14 -4.3656E+05 0.0000E+00 6.0385E+05 H1 5547
BOND = 1212.8072 ANGLE = 1376.2301 DIHED = 958.3127
VDWAALS = 8281.5188 EEL = -455552.3615 HBOND = 0.0000
1-4 VDW = 499.6376 1-4 EEL = 6667.0800 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
15 -4.3656E+05 0.0000E+00 6.0385E+05 H1 5547
BOND = 1212.8072 ANGLE = 1376.2301 DIHED = 958.3127
VDWAALS = 8281.5188 EEL = -455552.3615 HBOND = 0.0000
1-4 VDW = 499.6376 1-4 EEL = 6667.0800 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
16 -4.2997E+05 0.0000E+00 4.6458E+04 H2 11476
BOND = 1211.4884 ANGLE = 1375.6993 DIHED = 958.2583
VDWAALS = 8280.6225 EEL = -448967.2073 HBOND = 0.0000
1-4 VDW = 499.6253 1-4 EEL = 6667.0711 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
17 -4.2957E+05 0.0000E+00 2.4724E+04 H2 11476
BOND = 1212.3912 ANGLE = 1376.0627 DIHED = 958.2955
VDWAALS = 8280.3775 EEL = -448565.6392 HBOND = 0.0000
1-4 VDW = 499.6337 1-4 EEL = 6667.0772 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
18 -4.3346E+05 0.0000E+00 2.3093E+05 O 5624
BOND = 1212.6891 ANGLE = 1376.1826 DIHED = 958.3078
VDWAALS = 8281.1018 EEL = -452454.2624 HBOND = 0.0000
1-4 VDW = 499.6365 1-4 EEL = 6667.0792 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
19 -4.7082E+05 0.0000E+00 1.5606E+07 H1 5547
BOND = 1212.7709 ANGLE = 1376.2155 DIHED = 958.3112
VDWAALS = 8281.3825 EEL = -489813.4241 HBOND = 0.0000
1-4 VDW = 499.6372 1-4 EEL = 6667.0798 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
20 -4.5486E+05 0.0000E+00 6.0987E+06 O 5624
BOND = 1212.7479 ANGLE = 1376.2062 DIHED = 958.3103
VDWAALS = 8281.3019 EEL = -473858.6677 HBOND = 0.0000
1-4 VDW = 499.6370 1-4 EEL = 6667.0796 RESTRAINT = 0.0000
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
11 -4.5486E+05 0.0000E+00 6.0987E+06 O 5624
BOND = 1212.7479 ANGLE = 1376.2062 DIHED = 958.3103
VDWAALS = 8281.3019 EEL = -473858.6677 HBOND = 0.0000
1-4 VDW = 499.6370 1-4 EEL = 6667.0796 RESTRAINT = 0.0000
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.03 ( 0.67% of Total)
| Fast Water setup 0.00 ( 0.02% of Total)
| Build the list 0.46 (96.36% of List )
| Other 0.02 ( 3.64% of List )
| List time 0.48 (11.06% of Nonbo)
| Short_ene time 3.04 (99.18% of Direc)
| Other 0.03 ( 0.82% of Direc)
| Direct Ewald time 3.07 (79.35% of Ewald)
| Adjust Ewald time 0.05 ( 1.23% of Ewald)
| Fill Bspline coeffs 0.03 ( 4.04% of Recip)
| Fill charge grid 0.11 (15.05% of Recip)
| Scalar sum 0.13 (17.80% of Recip)
| Grad sum 0.22 (30.28% of Recip)
| FFT time 0.24 (32.83% of Recip)
| Other 0.00 ( 0.01% of Recip)
| Recip Ewald time 0.74 (19.15% of Ewald)
| Virial junk 0.00 ( 0.07% of Ewald)
| Other 0.01 ( 0.20% of Ewald)
| Ewald time 3.87 (88.94% of Nonbo)
| Nonbond force 4.35 (99.34% of Force)
| Bond/Angle/Dihedral 0.03 ( 0.64% of Force)
| Other 0.00 ( 0.02% of Force)
| Force time 4.37 (100.0% of Runmd)
| Runmd Time 4.37 (94.06% of Total)
| Other 0.24 ( 5.26% of Total)
| Total time 4.65 (100.0% of ALL )
| Highest rstack allocated: 1124788
| Highest istack allocated: 22930
| Job began at 15:23:07.617 on 12/03/2009
| Setup done at 15:23:07.789 on 12/03/2009
| Run done at 15:23:12.268 on 12/03/2009
| wallclock() was called 772 times
--------------------------------------------------------
AMBER SQM VERSION 1.0
By
Ross C. Walker (SDSC)
and
David A. Case (Rutgers)
--------------------------------------------------------
--------------------------------------------------------------------------------
3.1 QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 55
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
| QMMM: Parameter sets in use:
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: F : M.J.S.DEWAR et al. THEOCHEM, 180, 1, (1988)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: Cl: M.J.S.DEWAR et al. THEOCHEM, 180, 1, (1988)
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is disabled.
| QMMM: Using internal diagonalization routine (diag_routine=1).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 C 0.7280 1.4030 0.2550
QMMM: 2 2 H -0.1360 1.7560 0.7820
QMMM: 3 3 C 0.8030 0.0800 -0.1500
QMMM: 4 4 C -0.2900 -0.9320 0.1580
QMMM: 5 5 C -1.6350 -0.3520 0.0320
QMMM: 6 6 C -2.7180 0.1230 -0.0620
QMMM: 7 7 C -4.0440 0.6950 -0.1770
QMMM: 8 8 H -4.7410 0.3350 0.5580
QMMM: 9 9 C -4.6000 1.0130 -1.5410
QMMM: 10 10 H -5.6460 0.8200 -1.6970
QMMM: 11 11 H -3.9750 0.8060 -2.3900
QMMM: 12 12 C -4.2070 2.1230 -0.6290
QMMM: 13 13 H -4.9810 2.6990 -0.1550
QMMM: 14 14 H -3.3140 2.6760 -0.8580
QMMM: 15 15 C -0.1170 -1.5000 1.5820
QMMM: 16 16 F 1.0560 -2.0970 1.6930
QMMM: 17 17 F -0.1700 -0.5360 2.4800
QMMM: 18 18 F -1.0470 -2.3800 1.8660
QMMM: 19 19 O -0.2320 -2.0480 -0.7120
QMMM: 20 20 C 0.8930 -2.5380 -1.2450
QMMM: 21 21 O 0.9220 -3.6240 -1.7130
QMMM: 22 22 N 1.9640 -1.6960 -1.2420
QMMM: 23 23 H 2.7760 -2.0540 -1.6920
QMMM: 24 24 C 1.9190 -0.3690 -0.8360
QMMM: 25 25 C 2.9630 0.5030 -1.1140
QMMM: 26 26 H 3.8260 0.1540 -1.6530
QMMM: 27 27 C 2.8920 1.8170 -0.7000
QMMM: 28 28 H 3.6970 2.4940 -0.9110
QMMM: 29 29 C 1.7720 2.2620 -0.0180
QMMM: 30 30 Cl 1.6780 3.9240 0.4950
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
xmin cycle: 0 -92.1270 34.014819
xmin cycle: 1 -92.1270 34.014822
xmin cycle: 1 56.2537 100.607492
xmin cycle: 1 -108.4074 18.897440
xmin cycle: 2 171.4084 199.152083
xmin cycle: 2 -114.0974 9.777161
xmin cycle: 3 243.3936 224.330433
xmin cycle: 3 -116.0080 8.775533
xmin cycle: 4 -117.2529 4.816120
xmin cycle: 5 -118.2034 3.147941
xmin cycle: 6 -118.6802 3.418490
xmin cycle: 7 -118.8826 4.652237
xmin cycle: 8 -119.1775 1.610161
xmin cycle: 9 -119.2590 1.363163
xmin cycle: 10 -119.4107 1.936980
xmin cycle: 11 -119.4668 2.806109
xmin cycle: 12 -119.5340 0.909174
xmin cycle: 13 -119.5548 0.721331
xmin cycle: 14 -119.5836 0.693505
xmin cycle: 15 -119.6308 1.931021
xmin cycle: 16 -119.6752 0.846821
xmin cycle: 17 -119.6895 0.646653
xmin cycle: 18 -119.7186 0.559307
xmin cycle: 19 -119.6907 2.650203
xmin cycle: 19 -119.7296 0.790314
xmin cycle: 20 -119.7471 0.469740
xmin cycle: 21 -119.7644 0.493472
xmin cycle: 22 -119.7787 1.092135
xmin cycle: 23 -119.7995 0.369543
xmin cycle: 24 -119.8065 0.348270
xmin cycle: 25 -119.8212 0.834619
xmin cycle: 26 -119.8235 1.124273
xmin cycle: 27 -119.8322 0.395580
xmin cycle: 28 -119.8355 0.311420
xmin cycle: 29 -119.8531 0.424632
xmin cycle: 30 -119.8584 1.433298
xmin cycle: 31 -119.8791 0.452786
xmin cycle: 32 -119.8825 0.316890
xmin cycle: 33 -119.8881 0.353132
xmin cycle: 34 -119.8965 0.464396
xmin cycle: 35 -119.9048 1.235602
xmin cycle: 36 -119.9170 0.516126
xmin cycle: 37 -119.9246 0.403886
xmin cycle: 38 -119.9356 0.391660
xmin cycle: 39 -119.9499 0.521125
xmin cycle: 40 -119.9504 0.866068
xmin cycle: 40 -119.9555 0.342131
xmin cycle: 41 -119.9583 0.260274
xmin cycle: 42 -119.9625 0.312139
xmin cycle: 43 -119.9639 0.483778
xmin cycle: 44 -119.9661 0.180577
xmin cycle: 45 -119.9670 0.154163
xmin cycle: 46 -119.9683 0.171115
xmin cycle: 47 -119.9705 0.261225
xmin cycle: 48 -119.9719 0.147071
xmin cycle: 49 -119.9728 0.143206
xmin cycle: 50 -119.9753 0.194007
xmin cycle: 51 -119.9760 0.399475
xmin cycle: 52 -119.9777 0.159388
xmin cycle: 53 -119.9785 0.145888
xmin cycle: 54 -119.9847 0.301774
xmin cycle: 55 -119.9782 1.029864
xmin cycle: 55 -119.9863 0.247115
xmin cycle: 56 -119.9879 0.194899
xmin cycle: 57 -119.9921 0.337603
xmin cycle: 58 -119.9937 0.563189
xmin cycle: 59 -119.9973 0.264689
xmin cycle: 60 -120.0005 0.258710
xmin cycle: 61 -120.0041 0.326945
xmin cycle: 62 -120.0106 0.580285
xmin cycle: 63 -120.0159 0.282915
xmin cycle: 64 -120.0190 0.290138
xmin cycle: 65 -120.0248 0.345578
xmin cycle: 66 -120.0272 0.350165
xmin cycle: 67 -120.0291 0.201618
xmin cycle: 68 -120.0319 0.178047
xmin cycle: 69 -120.0354 0.480901
xmin cycle: 70 -120.0383 0.253911
xmin cycle: 71 -120.0402 0.189909
xmin cycle: 72 -120.0463 0.283609
xmin cycle: 73 -120.0477 0.706258
xmin cycle: 74 -120.0530 0.298320
xmin cycle: 75 -120.0555 0.213698
xmin cycle: 76 -120.0573 0.266116
xmin cycle: 77 -120.0618 0.386776
xmin cycle: 78 -120.0649 0.296344
xmin cycle: 79 -120.0676 0.271661
xmin cycle: 80 -120.0718 0.292370
xmin cycle: 81 -120.0746 0.210756
xmin cycle: 82 -120.0766 0.171846
xmin cycle: 83 -120.0786 0.225063
xmin cycle: 84 -120.0807 0.224809
xmin cycle: 85 -120.0826 0.201590
xmin cycle: 86 -120.0854 0.368246
xmin cycle: 87 -120.0872 0.212340
xmin cycle: 88 -120.0879 0.160397
xmin cycle: 89 -120.0895 0.138366
xmin cycle: 90 -120.0914 0.200248
xmin cycle: 91 -120.0930 0.221919
xmin cycle: 92 -120.0954 0.177987
xmin cycle: 93 -120.0992 0.245262
xmin cycle: 94 -120.0969 1.091463
xmin cycle: 94 -120.1018 0.441293
xmin cycle: 95 -120.1064 0.266721
xmin cycle: 96 -120.1106 0.245717
xmin cycle: 97 -120.1138 0.510311
xmin cycle: 98 -120.1191 0.268760
xmin cycle: 99 -120.1238 0.278250
xmin cycle: 100 -120.1284 0.565875
xmin cycle: 101 -120.1332 0.305166
xmin cycle: 102 -120.1349 0.275959
xmin cycle: 103 -120.1475 0.437191
xmin cycle: 104 -120.1478 0.878784
xmin cycle: 104 -120.1523 0.352453
xmin cycle: 105 -120.1555 0.281343
xmin cycle: 106 -120.1616 0.519732
xmin cycle: 107 -120.1673 0.290049
xmin cycle: 108 -120.1705 0.304046
xmin cycle: 109 -120.1730 0.901445
xmin cycle: 110 -120.1812 0.231026
xmin cycle: 111 -120.1824 0.213998
xmin cycle: 112 -120.1885 0.291762
xmin cycle: 113 -120.1922 0.447220
xmin cycle: 114 -120.1937 0.312115
xmin cycle: 115 -120.1947 0.176787
xmin cycle: 116 -120.1959 0.169774
xmin cycle: 117 -120.2052 0.279338
xmin cycle: 118 -120.1983 1.214470
xmin cycle: 118 -120.2078 0.375176
xmin cycle: 119 -120.2112 0.265829
xmin cycle: 120 -120.2148 0.410524
xmin cycle: 121 -120.2176 0.274082
xmin cycle: 122 -120.2200 0.177346
xmin cycle: 123 -120.2237 0.219459
xmin cycle: 124 -120.2271 0.491244
xmin cycle: 125 -120.2330 0.223497
xmin cycle: 126 -120.2360 0.260798
xmin cycle: 127 -120.2396 0.456574
xmin cycle: 128 -120.2458 0.286558
xmin cycle: 129 -120.2487 0.260043
xmin cycle: 130 -120.2547 0.379070
xmin cycle: 131 -120.2527 0.914406
xmin cycle: 131 -120.2581 0.320522
xmin cycle: 132 -120.2602 0.238828
xmin cycle: 133 -120.2630 0.242179
xmin cycle: 134 -120.2672 0.221755
xmin cycle: 135 -120.2707 0.306831
xmin cycle: 136 -120.2739 0.308909
xmin cycle: 137 -120.2787 0.256891
xmin cycle: 138 -120.2824 0.337356
xmin cycle: 139 -120.2860 0.241324
xmin cycle: 140 -120.2884 0.280174
xmin cycle: 141 -120.2894 0.227570
xmin cycle: 142 -120.2901 0.176397
xmin cycle: 143 -120.2929 0.176066
xmin cycle: 144 -120.2959 0.369684
xmin cycle: 145 -120.2982 0.223983
xmin cycle: 146 -120.2993 0.170325
xmin cycle: 147 -120.3010 0.172428
xmin cycle: 148 -120.3029 0.348329
xmin cycle: 149 -120.3047 0.166809
xmin cycle: 150 -120.3052 0.137478
xmin cycle: 151 -120.3074 0.135058
xmin cycle: 152 -120.3083 0.268298
xmin cycle: 153 -120.3092 0.130269
xmin cycle: 154 -120.3098 0.147514
xmin cycle: 155 -120.3114 0.130291
xmin cycle: 156 -120.3129 0.378140
xmin cycle: 157 -120.3143 0.154210
xmin cycle: 158 -120.3148 0.102160
xmin cycle: 159 -120.3155 0.092845
xmin cycle: 160 -120.3160 0.239252
xmin cycle: 161 -120.3168 0.100009
xmin cycle: 162 -120.3172 0.088746
xmin cycle: 163 -120.3177 0.124130
xmin cycle: 164 -120.3183 0.204176
xmin cycle: 165 -120.3187 0.100783
xmin cycle: 166 -120.3190 0.100644
xmin cycle: 167 -120.3196 0.092893
xmin cycle: 168 -120.3208 0.106864
xmin cycle: 169 -120.3212 0.193506
xmin cycle: 170 -120.3218 0.082583
xmin cycle: 171 -120.3221 0.087787
xmin cycle: 172 -120.3226 0.107331
xmin cycle: 173 -120.3227 0.255396
xmin cycle: 174 -120.3233 0.085676
xmin cycle: 175 -120.3234 0.058352
xmin cycle: 176 -120.3237 0.048725
xmin cycle: 177 -120.3241 0.050861
xmin cycle: 178 -120.3244 0.116277
xmin cycle: 179 -120.3249 0.120652
xmin cycle: 180 -120.3251 0.077717
xmin cycle: 181 -120.3253 0.067454
xmin cycle: 182 -120.3256 0.057619
xmin cycle: 183 -120.3258 0.045867
xmin cycle: 184 -120.3261 0.061477
xmin cycle: 185 -120.3264 0.143961
xmin cycle: 186 -120.3267 0.074177
xmin cycle: 187 -120.3268 0.070741
xmin cycle: 188 -120.3272 0.070562
xmin cycle: 189 -120.3275 0.063185
xmin cycle: 190 -120.3278 0.110459
xmin cycle: 191 -120.3279 0.087639
xmin cycle: 192 -120.3280 0.043700
xmin cycle: 193 -120.3281 0.039737
xmin cycle: 194 -120.3282 0.029338
xmin cycle: 195 -120.3282 0.042704
xmin cycle: 196 -120.3283 0.030400
xmin cycle: 197 -120.3283 0.029598
xmin cycle: 198 -120.3284 0.053463
xmin cycle: 199 -120.3284 0.031425
xmin cycle: 200 -120.3285 0.023012
xmin cycle: 201 -120.3285 0.023802
xmin cycle: 202 -120.3285 0.028957
xmin cycle: 203 -120.3286 0.051536
xmin cycle: 204 -120.3286 0.025362
xmin cycle: 205 -120.3286 0.030120
xmin cycle: 206 -120.3287 0.027041
xmin cycle: 207 -120.3288 0.037573
xmin cycle: 208 -120.3288 0.066770
xmin cycle: 209 -120.3289 0.030701
xmin cycle: 210 -120.3289 0.029554
xmin cycle: 211 -120.3290 0.046662
xmin cycle: 212 -120.3291 0.035858
xmin cycle: 213 -120.3292 0.031798
xmin cycle: 214 -120.3293 0.042790
xmin cycle: 215 -120.3293 0.080789
xmin cycle: 216 -120.3294 0.035757
xmin cycle: 217 -120.3295 0.027606
xmin cycle: 218 -120.3295 0.031297
xmin cycle: 219 -120.3296 0.079518
xmin cycle: 220 -120.3297 0.043256
xmin cycle: 221 -120.3298 0.033884
xmin cycle: 222 -120.3300 0.050183
xmin cycle: 223 -120.3298 0.169219
xmin cycle: 223 -120.3300 0.051105
xmin cycle: 224 -120.3301 0.040016
xmin cycle: 225 -120.3302 0.065864
xmin cycle: 226 -120.3303 0.075853
xmin cycle: 227 -120.3304 0.041189
xmin cycle: 228 -120.3305 0.037985
xmin cycle: 229 -120.3306 0.038004
xmin cycle: 230 -120.3308 0.111418
xmin cycle: 231 -120.3310 0.052493
xmin cycle: 232 -120.3310 0.042301
xmin cycle: 233 -120.3312 0.076022
xmin cycle: 234 -120.3313 0.049401
xmin cycle: 235 -120.3314 0.042261
xmin cycle: 236 -120.3316 0.079826
xmin cycle: 237 -120.3317 0.071052
xmin cycle: 238 -120.3318 0.049514
xmin cycle: 239 -120.3319 0.053540
xmin cycle: 240 -120.3320 0.056886
xmin cycle: 241 -120.3321 0.044391
xmin cycle: 242 -120.3323 0.048066
xmin cycle: 243 -120.3325 0.088650
xmin cycle: 244 -120.3326 0.050425
xmin cycle: 245 -120.3327 0.046515
xmin cycle: 246 -120.3328 0.060577
xmin cycle: 247 -120.3330 0.075068
xmin cycle: 248 -120.3331 0.179933
xmin cycle: 249 -120.3333 0.058192
xmin cycle: 250 -120.3334 0.046248
xmin cycle: 251 -120.3336 0.055786
xmin cycle: 252 -120.3335 0.253891
xmin cycle: 252 -120.3339 0.115239
xmin cycle: 253 -120.3341 0.051498
xmin cycle: 254 -120.3342 0.048563
xmin cycle: 255 -120.3346 0.130022
xmin cycle: 256 -120.3347 0.161591
xmin cycle: 257 -120.3350 0.056426
xmin cycle: 258 -120.3351 0.050402
xmin cycle: 259 -120.3354 0.068055
xmin cycle: 260 -120.3356 0.146515
xmin cycle: 261 -120.3359 0.067424
xmin cycle: 262 -120.3360 0.057021
xmin cycle: 263 -120.3362 0.056417
xmin cycle: 264 -120.3364 0.053551
xmin cycle: 265 -120.3366 0.090195
xmin cycle: 266 -120.3369 0.076790
xmin cycle: 267 -120.3371 0.069946
xmin cycle: 268 -120.3374 0.069887
xmin cycle: 269 -120.3378 0.105595
xmin cycle: 270 -120.3381 0.117940
xmin cycle: 271 -120.3383 0.081261
xmin cycle: 272 -120.3387 0.086897
xmin cycle: 273 -120.3388 0.118528
xmin cycle: 274 -120.3390 0.084112
xmin cycle: 275 -120.3395 0.061149
xmin cycle: 276 -120.3397 0.060384
xmin cycle: 277 -120.3399 0.085538
xmin cycle: 278 -120.3401 0.050482
xmin cycle: 279 -120.3404 0.072620
xmin cycle: 280 -120.3404 0.180725
xmin cycle: 281 -120.3407 0.058788
xmin cycle: 282 -120.3409 0.044387
xmin cycle: 283 -120.3410 0.048667
xmin cycle: 284 -120.3412 0.085525
xmin cycle: 285 -120.3414 0.055216
xmin cycle: 286 -120.3414 0.040382
xmin cycle: 287 -120.3416 0.039834
xmin cycle: 288 -120.3418 0.083230
xmin cycle: 289 -120.3418 0.104688
xmin cycle: 290 -120.3420 0.048214
xmin cycle: 291 -120.3421 0.037752
xmin cycle: 292 -120.3422 0.046777
xmin cycle: 293 -120.3423 0.083825
xmin cycle: 294 -120.3424 0.035460
xmin cycle: 295 -120.3424 0.031395
xmin cycle: 296 -120.3425 0.039192
xmin cycle: 297 -120.3426 0.032611
xmin cycle: 298 -120.3427 0.034236
xmin cycle: 299 -120.3428 0.085648
xmin cycle: 300 -120.3428 0.064901
xmin cycle: 301 -120.3429 0.024337
xmin cycle: 302 -120.3429 0.022094
xmin cycle: 303 -120.3430 0.027608
xmin cycle: 304 -120.3430 0.070290
xmin cycle: 304 -120.3430 0.033630
xmin cycle: 305 -120.3430 0.022799
xmin cycle: 306 -120.3431 0.018186
xmin cycle: 306 -120.3431 0.018186
Final SCF energy is -120.343061823631
Atomic Charges for Step 1 :
Atom Element Mulliken Charge
1 C -0.053
2 H 0.170
3 C -0.169
4 C 0.262
5 C -0.228
6 C -0.014
7 C -0.091
8 H 0.148
9 C -0.186
10 H 0.120
11 H 0.122
12 C -0.191
13 H 0.119
14 H 0.120
15 C 0.412
16 F -0.156
17 F -0.160
18 F -0.143
19 O -0.216
20 C 0.410
21 O -0.306
22 N -0.329
23 H 0.270
24 C 0.116
25 C -0.172
26 H 0.149
27 C -0.067
28 H 0.156
29 C -0.097
30 Cl 0.004
Total Mulliken Charge = 0.000
Final Structure
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 C 0.8731 1.2889 0.5647
QMMM: 2 2 H 0.1171 1.5543 1.3243
QMMM: 3 3 C 0.8272 0.0281 -0.0355
QMMM: 4 4 C -0.2594 -0.9406 0.3336
QMMM: 5 5 C -1.5664 -0.3705 0.1056
QMMM: 6 6 C -2.6532 0.0856 -0.1043
QMMM: 7 7 C -3.9443 0.6216 -0.3174
QMMM: 8 8 H -4.6883 0.2278 0.4113
QMMM: 9 9 C -4.4213 0.9176 -1.7226
QMMM: 10 10 H -5.4743 0.6930 -1.9701
QMMM: 11 11 H -3.7444 0.7148 -2.5715
QMMM: 12 12 C -4.1084 2.0483 -0.7943
QMMM: 13 13 H -4.9340 2.6455 -0.3676
QMMM: 14 14 H -3.2067 2.6595 -0.9763
QMMM: 15 15 C -0.1281 -1.3724 1.8761
QMMM: 16 16 F 1.1032 -1.8822 2.1886
QMMM: 17 17 F -0.3273 -0.3484 2.7627
QMMM: 18 18 F -1.0179 -2.3416 2.2450
QMMM: 19 19 O -0.2123 -2.2127 -0.3416
QMMM: 20 20 C 0.7252 -2.4801 -1.3146
QMMM: 21 21 O 0.5865 -3.5920 -1.8345
QMMM: 22 22 N 1.7161 -1.5630 -1.6354
QMMM: 23 23 H 2.3863 -1.8166 -2.3257
QMMM: 24 24 C 1.7861 -0.3175 -1.0159
QMMM: 25 25 C 2.7955 0.6105 -1.3595
QMMM: 26 26 H 3.5540 0.3514 -2.1140
QMMM: 27 27 C 2.8342 1.8545 -0.7466
QMMM: 28 28 H 3.6244 2.5730 -1.0186
QMMM: 29 29 C 1.8721 2.1961 0.2119
QMMM: 30 30 Cl 1.9212 3.7241 0.9483
--------- Calculation Completed ----------
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Fri Dec 04 2009 - 19:30:02 PST
