[AMBER-Developers] Possible bug with ntt=3 and ntr=1

From: Ross Walker <ross.rosswalker.co.uk>
Date: Tue, 7 Jul 2009 07:15:00 +0100

Hi All,

I am trying to track down what I think is a bug with GB runs where ntt=3 and
harmonic restraints (ntr=1) are in use. I am currently seeing weird behavior
with simulations of the nucleosome in GB where I am restraining just the
DNA. With gamma_ln >= 1.0 the system is stable but the dynamics is plain
wrong. As I reduce gamma_ln the system becomes more and more unstable. This
is strange since it would seem to me that as gamma_ln tends towards zero is
should approximate NVE which in this case is completely stable.

My input file looks like this:

&cntrl
  imin=0,irest=1,ntx=5,
  nstlim=250000,dt=0.002,
  ntf=2,ntc=2,ntb=0,
  igb=5,cut=10.0,rgbmax=10.0,
  ntpr=100,ntwx=100,ntwr=10000,
  ntr=1,saltcon=0.1,
  tempi=310.0,temp0=310.0,
  ntt=3,gamma_ln=0.001,
  ig=1037891,
 /
RESTRAIN DNA
0.5
RES 1 294
END
END

In this case with gamma_ln=0.001 the system crashes after 3100 steps with a
temperature of 4800K!. This is true both of sander and pmemd.

Interestingly if I turn off restraints all is fine. Similarly if I set ntt=0
(NVE) all is fine. Example outputs are attached.

       mdout.orig = pmemd with ntt=3, ntr=1
mdout.orig.sander = sander with ntt=3, ntr=1
  mdout.orig.ntr0 = pmemd with ntt=3, ntr=0
   mdout.orig.nve = pmemd with ntt=0, ntr1

Interestingly everything looks good until NSCM is triggered at step 1000.

NSTEP = 900 TIME(PS) = 101.800 TEMP(K) = 308.05 PRESS =
0.0
 Etot = -66743.9688 EKtot = 19528.7840 EPtot =
-86272.7528
 BOND = 5722.9654 ANGLE = 13508.0515 DIHED =
17017.8931
 1-4 NB = 5619.2367 1-4 EEL = 1382.5208 VDWAALS =
-13061.4667
 EELEC = -73648.3380 EGB = -43368.0253 RESTRAINT =
554.4096
 EAMBER (non-restraint) = -86827.1624
 
----------------------------------------------------------------------------
--
| RE_POSITION Moving by  -0.484242 -0.548000 -0.613646
 NSTEP =     1000   TIME(PS) =     102.000  TEMP(K) =   306.89  PRESS =
0.0
 Etot   =    -66749.0252  EKtot   =     19454.8086  EPtot      =
-86203.8338
 BOND   =      5765.1339  ANGLE   =     13518.0488  DIHED      =
17010.2508
 1-4 NB =      5557.7458  1-4 EEL =      1277.5502  VDWAALS    =
-13007.4986
 EELEC  =    -74808.4224  EGB     =    -42038.1373  RESTRAINT  =
521.4950
 EAMBER (non-restraint)  =    -86725.3288
 
----------------------------------------------------------------------------
--
 NSTEP =     1100   TIME(PS) =     102.200  TEMP(K) =   365.32  PRESS =
0.0
 Etot   =    -62356.5394  EKtot   =     23159.5258  EPtot      =
-85516.0652
 BOND   =      5762.5203  ANGLE   =     13597.3821  DIHED      =
17100.7761
 1-4 NB =      5590.5033  1-4 EEL =      1324.8176  VDWAALS    =
-12951.1683
 EELEC  =    -77138.7949  EGB     =    -39800.5919  RESTRAINT  =
998.4905
 EAMBER (non-restraint)  =    -86514.5557
 
----------------------------------------------------------------------------
--
The restraint energy then takes a jump and the system never recovers and the
temperature just keeps rising.
Thus I think the problem is related to NSCM recentering the system and not
allowing for restraints properly.
Running the simulation with nscm explicitly set to 0 also appears to fix the
problem.
mdout.orig.nscm0.bz2
Inspection of the re-centering routine (in both PMEMD and sander) shows that
there is a call to re_position:
which should execute the following code:
  if (master) &
    write(mdout, '(a, 3f10.6)')"| RE_POSITION Moving by ", xd, yd, zd
  vec(1) = vec(1) + xd
  vec(2) = vec(2) + yd
  vec(3) = vec(3) + zd
  do i = 1, n
    x(1,i) = xd + x(1,i)
    x(2,i) = yd + x(2,i)
    x(3,i) = zd + x(3,i)
  end do
  if (ntr .gt. 0) then
    do i = 1, n
      xr(1,i) = xd + xr(1,i)
      xr(2,i) = yd + xr(2,i)
      xr(3,i) = zd + xr(3,i)
    end do
  end if
However, in both sander and PMEMD ntr has been hard coded to be zero inside
this routine:
          call re_position(atm_cnt, 0, crd, crd, vcm(1), vcm(2), vcm(3), &
                           sys_x, sys_y, sys_z, sys_range, 0)
subroutine re_position(n, ntr, x, xr, xc, yc, zc, x0, y0, z0, vec, verbose)
Thus I tried changing this to execute the above code when ntr=1 and ntt=3
which it would seem should fix the problem but alas it does not:
mdout.mod.bz2
Thus it would seem that ntr=1 with ntt=3 and nscm = 1000 (default) is
broken. However, the fact that the re_positioning code exists for ntr=1 and
ntt=3 but has been hard wired to not be used means that someone at least was
aware of the situation.
Comments / suggestions for fixes anyone?
All the best
Ross
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk | 
| http://www.rosswalker.co.uk | PGP Key available on request |
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Received on Tue Jul 07 2009 - 01:07:23 PDT
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