On Mon, Jun 25, 2012 at 2:00 PM, DEBOSTUTI GHOSHDASTIDAR <
debostutighosh.gmail.com> wrote:
> Hello Prof Case,
>
> There are no zero LJ epsilons in the force field. I am attaching the
> frc file for the molecule which is showing SHAKE error. It is an
>
I don't think this is true. All hydrogen atoms attached to oxygens have 0s
for the LJ parameters in the Amber force fields (waters, hydroxyls,
carboxylic acids, etc.).
You can use xparmed.py (from AmberTools 12) to dump out a complete frcmod
file for every parameter/atom type present in your topology to verify this..
acetate anion. In vmd i do not see anything unusual in this atoms even
> after setting ntwx=1.
I'm not sure what you're seeing here. It is still crashing, but you don't
see anything in VMD after you set ntwx=1? Or it's no longer crashing after
you set ntwx=1?
HTH,
Jason
>
> Thank you
>
> Debostuti
> On 6/23/12, David A. Case <case.biomaps.rutgers.edu> wrote:
> > On Wed, Jun 20, 2012, DEBOSTUTI GHOSHDASTIDAR wrote:
> >>
> >> The system comprises
> >> of dna dodecamer in a solvent, the parameters for which were partly
> >> developed by our group (published work) and partly obtained from
> >> literature. When I ran the solvent alone with the same number of
> >> solvent molecules as the system under question but without dna, it
> >> showed a "vlimit exceeded" error during the first NPT run.
> >
> > This sounds like a problem with the solvent force field, but people on
> the
> > list won't have enough information to solve the problem. Look for
> > hydrogens
> > with zero LJ epsilons. Stop the simulation right before (i.e. one step
> > before
> > the crash), or set ntwx=1, and examine the structures you have. It seems
> > possible (or likely) that you have some unacceptably close atom contacts,
> > and
> > you will have to figure out where they are coming from.
> >
> > ....dac
> >
> >
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> >
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jun 25 2012 - 12:30:02 PDT
