Hello Prof Case
The system crashed after 14000 steps and ntwx=1000. So I continued the
run with ntwx=1 and this time the crash was after 311 steps. This time
SHAKE error was for atoms 1678 and 1679. These are the same atoms as
8261 and 8262, but belonging to another residue. 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. A dilute
solution without the dna is however running fine. Could this be a
problem due to overpacking?The atoms under question do belong to the
solvent and therefore fall in the non standard region. Could I send
the files to your personal id, since even the last few trajectories
exceed the file limit I am allowed to post to this group and the mail
is bouncing back.
Thank you so much for all your help
Debostuti
On 6/18/12, David A. Case <case.biomaps.rutgers.edu> wrote:
> On Mon, Jun 18, 2012, DEBOSTUTI GHOSHDASTIDAR wrote:
>>
>> I had been running the system with dt=0.001. However, after 1ns
>> simulation when I increased dt to 0.002fs, it crashed with the
>> following error:
>>
>> Coordinate resetting (SHAKE) cannot be accomplished,
>> deviation is too large
>> NITER, NIT, LL, I and J are : 0 1 5407 8261 8262
>>
>> Note: This is usually a symptom of some deeper
>> problem with the energetics of the system.
>
> Does it immediately crash (i.e. on the first step where you have the
> increased
> time step? Or sometime well into the simulation? It might help to look at
> the system right before the SHAKE error occurs. It would also be of some
> help
> to know if this is a standard system (protein/nucleic acid) or has
> non-standard parts like ligands or cofactors; and if atoms 8261 and 8262
> are
> in (or close to) any non-standard region.
>
> ....dac
>
>
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Received on Wed Jun 20 2012 - 10:00:02 PDT
