[gmx-users] em and nvt problem

[Daniel Kozuch]

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
> --
> 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.
>