[gmx-users] Graphene topology file

Justin Lemkul jalemkul at vt.edu
Thu Jul 17 13:51:50 CEST 2014

On 7/17/14, 7:16 AM, #SUKRITI GUPTA# wrote:
> Hi gromacs users,
> I read that for slab geometries where you need pbc in xy, you can use pbc=xyz and have a slab of vacuum
> in between the periodic images in z and use ewald3dc (Yeh and Berkowitz method). So I changed my mdp file extended my box in z direction( with no solvent molecules) and did the energy minimization and npt again. In em, the box looks fine but with npt again I get same output i.e. water molecules fly away and box size in z direction increases drastically, through the vacuum layer is still maintained. Then I changed my pressure coupling to Parinello- Rahman instead of Berendsen. This time npt runs some steps and gives an error message:
> Fatal error:
> One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.
> Can anyone please let me know how can I solve this problem. If we have a layer of vacuum, wont the box size reduce in npt and cause this error? Should I skip npt and directly do nvt?

If you need to maintain a vacuum layer, your box needs to be incompressible 
along that direction, i.e. use semiisotropic coupling and set compressibility = 
0 in the .mdp file for the z-direction.



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


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