[gmx-users] Graphene sheet topology

soumadwip ghosh soumadwipghosh at gmail.com
Sun Apr 24 14:48:12 CEST 2016

Thanks Justin as always for your prompt reply.

I have now created the graphene topology the way u suggested that is I
issued the following command

1. g_x2top -f file.gro -o graphene.top -pbc: I did not prefer to use the
-noparam option since it does not print the k0, k1 and similar values.

2. I have now started the simulation with all my mdp files (ions.mdp,
minim.mdp, nvt.mdp, npt.mdp and md.mdp) containing the "periodic
molecules=yes" line and as of now the simulation is running fine. But the
last one crashed around 25 ns showing the Lincs warnings and stuffs so
keeping my fingers crossed.

3. I am keeping the dihedral function type 1 as per your suggestion.

Please let me know if what I am doing right now as mentioned above makes
sense or not. I will update on the outcomes of my simulation even if
everything goes right.

Thanks once again for the reply Justin..:)

Soumadwip Ghosh
Senior Research Fellow
Indian Institute of Technology Bombay

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