[gmx-users] em and nvt problem

[Marlon Sidore]

You can try to reduce emtol in your minimization parameters or start your
nvt at a different, lower, temperature.

Best,

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France


2017-05-25 15:05 GMT+02:00 Daniel Kozuch <dkozuch at princeton.edu>:

> It would be helpful if you include the output of the em run and the log
> file for the nvt run.
>
> Best,
> Dan
>
> On Thu, May 25, 2017 at 7:12 AM, Kashif <kashifzamir180.mk at gmail.com>
> wrote:
>
> > Hi
> > Whenever I tried to simulate one of my docked complex, the energy
> > minimization step converged very fast and complete at 112 steps. And
> when I
> > proceed with NVT equilibration I got split structures like ........
> > step4b_n6.pdb
> > step4c_n6.pdb
> > step5b_n6.pdb
> > step5c_n6.pdb
> >
> > I have already docked the drug with my protein using different tool in
> > order to get different docked pose of drug. So that I could get different
> > topology file and coordinate file of the drug from PRODRG server.
> > But the same problem encounters.
> > Some time I got the error like .........
> >
> > Fatal error:
> > 1 particles communicated to PME node 5 are more than 2/3 times the
> cut-off
> > out of the domain decomposition cell of their charge group in dimension
> y.
> > This usually means that your system is not well equilibrated.
> > ........................................................
> >
> > kindly help
> >
> > regards
> > kashif
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