[gmx-users] Graphene sheet topology

Justin Lemkul jalemkul at vt.edu
Sun Apr 24 13:58:49 CEST 2016

On 4/23/16 1:37 AM, soumadwip ghosh wrote:
> Hello all,
>               I am currently working on the interaction between a flat
> graphene sheet and nucleic acids at various physiological conditions. I am
> using CHARMM 27 force field and GROMACS 4.5.6 for MD simulations. Here is
> my work order
> 1. I created a graphene.top file according to the tutorial by Andrea Minoia.
> 2. I went upto NPT equilibration without any problem but my MDrun crashes
> printing the following error (I modified the .n2t and other CHARMM 27
> forcefield files according to the tutorial)
> Fatal error:
> 25 particles communicated to PME node 4 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
>  From the mails in the mailing list I am assuming that my graphene topology
> has something terribly bad since I have worked with the particular nucleic
> acid in CHARMM27 and it does not have any issue. I am uploading the pdb and
> itp files of my graphene sheet followed by the md.mdp and md.log file. Any
> kind of help to troubleshoot this error would be greatly appreciated.
> pdb file of graphene:
> https://drive.google.com/open?id=0B7SBnQ5YXQSLQWVod3psQTFwSzg
> graphene.itp: https://drive.google.com/open?id=0B7SBnQ5YXQSLTXlqci1aX3NzU3c
> the visualization of graphene.pdb:
> https://drive.google.com/open?id=0B7SBnQ5YXQSLMExiSG5GR3VIMjA
> My md.mdp file:
> https://drive.google.com/open?id=0B7SBnQ5YXQSLMmd1di1jbHpubFE
> the md.log file I obtained:
> https://drive.google.com/open?id=0B7SBnQ5YXQSLdXZDZVNDOFJqVDg
> PS: I forgot to issue the -pbc while executing the g_x2top command and also
> did not change the dihedral function type from 1 to 3 as suggested in the
> tutorial. Can this be a reason for the above error to occur?

Your sheet appears to be periodic, so yes, you need to treat it as such (also by 
adding "periodic_molecules = yes" in the .mdp file).  Otherwise, your atoms are 
at very close distance at the box edges and things explode.

CHARMM uses periodic dihedrals, so the function type is 1 (though we usually use 
9 because CHARMM often applies multiple terms to each dihedral).  But if you 
only have one multiplicity per dihedral, type 1 is fine (and setting it to 9 
would be equivalent in this case).



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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