[gmx-users] Nano-structures equilibration

Alex nedomacho at gmail.com
Sun Jul 2 21:12:09 CEST 2017

You have problems with the system and you expect everyone here to be a 
magician and guess your inputs. What is the forcefield, what is the 
timestep, how are you describing your graphene sample, what is your 
number of exclusions for that sample, what is your barostat type during 
eqilibration? Are you doing static energy minimization prior to your 
equilibration run?


On 7/1/2017 11:58 PM, ‪Mohammad Roostaie‬ ‪ wrote:
> Thank you very much, Alex. I also performed the process on GPU, and I got the below error:
> step 1: Water molecule starting at atom 96743 can not be settled.Check for bad contacts and/or reduce the timestep if appropriate.Wrote pdb files with previous and current coordinates
> WARNING: Listed nonbonded interaction between particles 4321 and 4328at distance 21.231 which is larger than the table limit 1.853 nm.
> This is likely either a 1,4 interaction, or a listed interaction insidea smaller molecule you are decoupling during a free energy calculation.Since interactions at distances beyond the table cannot be computed,they are skipped until they are inside the table limit again. You willonly see this message once, even if it occurs for several interactions.
> IMPORTANT: This should not happen in a stable simulation, so there isprobably something wrong with your system. Only change the table-extensiondistance in the mdp file if you are really sure that is the reason.
> I would appreciate any help.
> Regards,Mohammad
>        From: Alex <nedomacho at gmail.com>
>   To: gmx-users at gromacs.org
>   Sent: Friday, 30 June 2017, 22:21:26
>   Subject: Re: [gmx-users] Nano-structures equilibration
> You have performance-related errors, maybe try a different number of
> ranks, or another machine, or OpenMP instead of MPI -- hope others will
> be able to comment on technical issues.
> Your question was whether you should abandon nanostructure equilibration
> because of this -- the answer is of course no.
> Alex
> On 6/30/2017 5:03 AM, Mohammad Roostaie wrote:
>> I asked it since I got some errors regarding the NPT equilibration,
>> also this link says that turn off the pressure coupling.
>> The errors which I received is as follow:
>> Fatal error:
>> The number of ranks you selected (14) contains a large prime factor 7.
>> In most cases this will lead to bad performance. Choose a number with
>> smaller prime factors or set the decomposition (option -dd) manually.
>> For more information and tips for troubleshooting, please check the
>> website at http://www.gromacs.org/Documentation/Errors
>> —---------------------------------------------------—
>> Halting parallel program mdrun_mpi on rank 0 out of 14
>> —------------------------------------------------------------------------
>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>> with errorcode 1.
>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>> You may or may not see output from other processes, depending on
>> exactly when Open MPI kills them.
>> Furthermore, I used -dd (with the values of 7 2 1) option, and I got
>> this error:
>> Fatal error:
>> 1130 particles communicated to PME rank 14 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.
>> For more information and tips for troubleshooting, please check the
>> website at Errors - Gromacs
>> Regards,
>> M
>> ------------------------------------------------------------------------
>> On Friday, June 30, 2017, 12:47:05 PM GMT+4:30, Alex
>> <nedomacho at gmail.com> wrote:
>> Is this a philosophical question? Yes, it is certainly possible for
>> graphene+peptide to exist in water under pressure.
>> On 6/30/2017 12:05 AM, Mohammad Roostaie wrote:
>>> Hi All,
>>> Is it possible and necessary to run NPT equilibration process on the
>> nanostructure systems (graphene+peptide in water)? Since I got some
>> errors regarding this process.
>>> Regards,Mohammad

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