[gmx-users] Re: Creating an infinite sheet of graphene

[Justin Lemkul]

On 8/29/13 7:43 AM, Valentina wrote:
> Hi,
>
> I have no answer to this question, sorry.
>
> But I am trying to simulate the layered structure (also with
> periodic_molecule = yes)
>
> I am getting error:
>
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+01
>     Number of steps    =          500
>
> A list of missing interactions:
>            exclusions of    535 missing     48
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.5
> Source code file: domdec_top.c, line: 173
>
> Software inconsistency error:
> Some interactions seem to be assigned multiple times
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
>
> While I do not have this problem when simulating without periodic_molecule =
> yes.
>
>
> I think this is along similar lines of problem,

If you have a question of your own, please start a new topic rather than hijack 
someone else's thread.

The problem lies somewhere in the topology, but you haven't told us (1) what the 
system is, (2) how you generated its topology, or (3) what is in the topology.

I would recommend you start a new thread (to avoid confusing cross-talk with the 
OP's question) with all of that information.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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