[gmx-users] position resrtraints

[Justin Lemkul]

On 5/18/15 8:47 AM, soumadwip ghosh wrote:
> Dear Justin,
>                  thanka 4 ur prompt reply. I checked that there was
> another issue. I didnot modify the aminoacids.rtp file in order to
> incorporate the new graphene.pdb atom types according to the force
> field. It appears to me that the correct interaction is not arsising
> because the atoms mentioned in the PDB file is alien to the force
> field. Is it the case? Should I modify the aminoacids .rtp file to

None of this makes any sense to me.

> account for the sp2 carbon atoms and the terminal hydrogens mentioned
> in the PDB file and then procced without really bothering about
> pdb2gmx and position restraints? I think I made a very silly mistake
> to begin with.
>

I really don't know how restraints factor in here.  You have a suboptimal force 
field and an inadequate simulation time to observe the phenomenon you want. 
Those are your primary problems.

-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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