Hi
Thanks. i'll surely try doing it and check the output.
first occurrence of vlimit exceeds appears at step 159, so it runs properly
till 158 steps.
My temperature limits are 0 to 300. and i observe that in all those steps
where vlimit exceeds, temperature blows off beyond 300. Could this be the
reason for vlimit exceeding? if yes, what could be the reason for that?
On Wed, Oct 3, 2012 at 7:23 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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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>
--
Jitesh V. Doshi
Research Associate,
Bioinformatics Centre,
University of Pune.
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Received on Fri Oct 05 2012 - 00:00:02 PDT
