Dear Case:
thank you very much for kind reply.
I've also tried to run NVT before NPT with following parameters, however,
it also stacked in 1000 steps.
heating gradually over 600ps
&cntrl
imin=0,irest=0,ntx=1,
nstlim=600000,dt=0.001,
ntc=2,ntf=2,
cut=10.0, ntb=1,
ntpr=100, ntwx=100,
ntt=3, gamma_ln=2.0,
tempi=0.0, temp0=310.0,
restraintmask=':1-396 &!.H=',
restraint_wt=30.0,
iwrap=1,
ig=-1,
nmropt=1,
/
&wt TYPE='TEMP0', istep1=0, istep2=300000,
value1=0.1, value2=310.0, /
&wt TYPE='END' /
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
wrapping first mol.: -63.01100 0.00000 -110.58600
wrapping first mol.: -63.01100 0.00000 -110.58600
NSTEP = 1000 TIME(PS) = 1.000 TEMP(K) = 2.22 PRESS =
0.0
Etot = -129869.8642 EKtot = 213.8130 EPtot =
-130083.6772
BOND = 199.7600 ANGLE = 1492.0223 DIHED =
4917.7727
1-4 NB = 1995.9734 1-4 EEL = 2355.5850 VDWAALS =
9656.9198
EELEC = -150701.7104 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
2012/7/14 case <case.biomaps.rutgers.edu>
> On Fri, Jul 13, 2012, Albert wrote:
> >
> > I am using the following command and input file to run NPT
> >
> > *mpiexec -np 2 $AMBERHOME/bin/pmemd.cuda.MPI -O -p apo.prmtop -c m6.rst
> > -ref m6.rst -i npt1.in -o npt1.out -r npt1.rst -x npt1.mdcrd -inf
> npt1.info*
> > *
> > *
> > *equilibration*
> > * &cntrl*
> > * imin=0, irest=0, ntx=1,*
> > * nstlim=500000, dt=0.002,*
> > * ntc=2, ntf=2,*
> > * cut=10.0, *
> > * ntb=2, ntp=3, taup=2.0, pres0=1,*
> > * ntpr=5000, ntwx=5000, ntwr=50000,*
> > * ntt=3, gamma_ln=1.0, ig=-1,*
> > * iwrap=1,*
> > * temp0=310.0,*
> > * csurften=3, ninterface=2, gamma_ten=17,*
> > * restraintmask='1-396 &!.H',*
> > * restraint_wt=20,*
> > * /*
> >
> > however, I found that the npt1.out and npt1.info stacked there after
> > several hours of running:
>
> Usual instructions for debugging MD:
>
> 1. Set nstlim=50 and ntpr=1. If that works, you can start increasing
> both variables. If it fails, you may have more information, or go to the
> next
> step.
>
> 2. For the short run cited above, start with a single thread cpu run. Then
> try in parallel on a cpu; then in serial mode on the GPU; see if there is
> something that works and something that fails.
>
> Specific to your situation:
>
> Equilibrate first a constant volume until you get a temperature somewhat
> near
> your final temperature; then turn on constant pressure. You are asking
> for constant pressure simulations with an intial temperature of zero, which
> can lead to unstable behavior.
>
> FWIW, I always do initial system preparation and some amount of
> equilibration
> on a cpu...lots of bad things can happen right at the beginning (sometimes
> driven by my poor choices of input variables.) Once I'm confident that the
> input files are giving acceptable outputs, I'll start increasing nstlim and
> consider moving things to a GPU.
>
> ...good luck....dac
>
>
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Received on Fri Jul 13 2012 - 23:00:03 PDT
