[gmx-users] position rstraints

[Justin Lemkul]

On 5/18/15 6:55 AM, soumadwip ghosh wrote:
> 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

30 ns is a very short amount of time.

> because I dint do the pdb2gmx of the graphene separately so the accurate
> atomic level interaction is not following? Does the non-incorporation of

No, that's not a problem at all.  There is no requirement to use pdb2gmx at all.

> 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?
>

There are two possible issues: (1) your simulation is too short and/or (2) the 
force field is not a good one.  I don't know of any papers that have used 53A5 
(which is designed for hydrophobic solvents) for DNA; recent version of CHARMM 
and AMBER are much better force fields for nucleic acid simulations.

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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