[gmx-users] position rstraints

soumadwip ghosh soumadwipghosh at gmail.com
Mon May 18 12:55:45 CEST 2015

Hi all,

       I am trying to see the unzipping of double stranded DNA on the
surface of graphene nanosheets. I am using GROMOS 53a5 force field and I
obtained a graphene sheet from ATB software. i obtained both the .itp as
well as the PDB from that site. Now, I proceeded for molecular dynamics
withou doing pdb2gmx and without any posre file for the graphene. The dsDNA
and the graphene coordinates were concatenated and throughout the
euilibration and mdrun it dint give any trouble. However, after 30 ns of
the mdrun, I am observing no unzipping of the DNA chain and the no.of
H-bond between the parallel strands remain unchanged. Is it happening
because I dint do the pdb2gmx of the graphene separately so the accurate
atomic level interaction is not following? Does the non-incorporation of
the posre_graphene file in the dynamics has anuthing to do with it? Should
I restart after doing pdb2gmx of the graphene , obtaining the
posre_graphene file and include it in the graphene.itp file provided by the
ATB server?

Your help is required. Hope I am not asking for much.

Research Fellow,
IIT Bombay,

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