On Wed, Oct 03, 2012, Jitesh Doshi wrote:
> I am heating up my system from 0 through 300 K with following input
>
> Initial heating and equilabration
> &cntrl
> imin=0, irest=0, ntx=1,ig=-1,
> nstlim=100000, dt=0.001, ntc=1,
> ntpr=100, ntwx=10,
> ntr=1, restraint_wt=1, restraintmask=':1-356',
> cut=16, ntb=0, igb=0,
> ntt=3, gamma_ln=1.0,
> tempi=0.0, temp0=300.0,
> /
When you have problems, set nstlim=100, ntpr=1, and look carfully at the
output. It's not clear where your "vmax" problems first appear, but it seems
likely that there may be problems with the initial structure. (Did you carry
out energy minimization first?)
Note also that Amber is not particularly well suited to doing vacuum
simulations, but that fact is probably unrelated to the problems you are
seeing.
...dac
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Received on Wed Oct 03 2012 - 07:00:03 PDT
