[gmx-users] Adding metal ions near graphene sheet

Justin Lemkul jalemkul at vt.edu
Tue Aug 26 14:08:27 CEST 2014

On 8/26/14, 12:15 AM, #SUKRITI GUPTA# wrote:
> Dear Gromacs users,
> I want to simulate a system with graphene sheet with water around it
> containing some metal ions. I want these metal ions to be present very close
> to the graphene sheet. By using genbox or genion commands I can get ions to
> be inserted randomly in the system but not at the location I want them to be
> present. Can anyone please let me know if it is possible to get metal ions
> replace the water molecule from the region we want it to? I tried adding ion
> near the sheet by adding the ion in the graphene pdb file itself and also by
> firstly taking a small simulation box and adding ions using genbox and later
> expanding the box and filling it with water. But in both these cases, during
> energy minimization I get error that segmentation fault / core dumped.

This is a good approach.  If you got a crash/seg fault, you probably had bad 
contacts somewhere, so probably one of the randomly inserted ions was in a 
really bad spot (which should be easy to see in the pre-solvation coordinate file).

In theory, you could probably do the insertion with selections, specifying the 
closest waters within some cutoff of the graphene, but the simpler approach 
you've already tried can be made to work.



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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