[gmx-users] Graphene topology file

[Justin Lemkul]

On 7/7/14, 7:54 AM, #SUKRITI GUPTA# wrote:
> Hi Justin,
>
> Thanks for the reply. Actually I am having the problem of z- dimension to be
> zero only when I am giving pbc only in xy direction. For pbc in xyz, the z
> dimension is not becoming zero. So do you still think it can be because of
> improper box size chosen?
>

No, the z-dimension would not be relevant with pbc = xy.

> Also I have not given nwall option in .mdp file. As Abhijit suggested, it can
> create a problem. I do not have any idea about nwall functioning and what
> parameters to choose for it to work with xy periodic graphene sheet. I am
> unable to find any tutorial about this also. Can you please suggest me what
> to do for this.
>

The manual discusses walls in great detail, though they're not required in this 
case.  What reason do you have for only using 2-D PBC?  Why not 3-D (pbc = xyz)?

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================