yes.. i have run minimization in two steps.. restrained and then freeing
all the atoms. I am not sure as to how exactly I should start dissecting
the problem. Whatever i know about amber, things seems fine except I don't
know if something is wrong with the input file for the run which is:
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,
/
On Fri, Oct 5, 2012 at 5:28 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Fri, Oct 05, 2012, Jitesh Doshi wrote:
>
> > first occurrence of vlimit exceeds appears at step 159, so it runs
> properly
> > till 158 steps.
>
> This ain't necessarily so. It may just mean the problems with the setup
> don't
> become severe enough until then to trigger the warning.
>
> > 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?
>
> It's the other way around: bad forces or collisions are leading to large
> local
> velocities. This is turn results in high temperatures. All these are just
> symptoms....you need to examine your simulation carefully to look for what
> might be causing the problem. Did you indeed run energy minimization
> first?
>
> ...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 - 05:30:05 PDT
