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 Fri Jun 22 2012 - 16:00:04 PDT
