Hello ...
When the system was crashing, the SHAKE error output in the logfile
indicated problems with atoms which belonged to the anion part of the
solvent molecule. The force field for this solvent was developed by
us. I meant to say this solvent force field has no zero LJ epsilons
since it is an acetate anion.
Also I observed the two atoms (which were mentioned in the logfile for
the SHAKE error) on vmd after setting ntwx=1. The system still crashed
but there was nothing odd in these two atoms...am I missing something
here?
Thanks
Debostuti
On 6/26/12, Jason Swails <jason.swails.gmail.com> wrote:
> 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 - 23:30:03 PDT
