[gmx-users] em and nvt problem
marlon.sidore at gmail.com
Thu May 25 15:17:52 CEST 2017
You can try to reduce emtol in your minimization parameters or start your
nvt at a different, lower, temperature.
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
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.
> On Thu, May 25, 2017 at 7:12 AM, Kashif <kashifzamir180.mk at gmail.com>
> > 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
> > out of the domain decomposition cell of their charge group in dimension
> > This usually means that your system is not well equilibrated.
> > ........................................................
> > kindly help
> > regards
> > kashif
> > --
> > Gromacs Users mailing list
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users