[gmx-users] Graphene sheet topology

soumadwip ghosh soumadwipghosh at gmail.com
Sat Apr 23 07:37:36 CEST 2016

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:

graphene.itp: https://drive.google.com/open?id=0B7SBnQ5YXQSLTXlqci1aX3NzU3c

the visualization of graphene.pdb:

My md.mdp file:

the md.log file I obtained:

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?

Thanks and regards,
Soumadwip Ghosh
Senior Research Scholar
Indian Institute of Technology Bombay

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