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
acetate anion. In vmd i do not see anything unusual in this atoms even
after setting ntwx=1.
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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Received on Mon Jun 25 2012 - 11:30:02 PDT
