[gmx-users] (no subject)

Justin Lemkul jalemkul at vt.edu
Tue Oct 6 16:48:27 CEST 2015

On 10/6/15 1:43 AM, saranya wrote:
> GROMACS users,
> I was trying to perform a MD simulation of a system with a protein with Ag+
> metal ion but realized that GROMACS does not  have parameters for the Ag+
> ion. I tried to include the parameters in the ion.itp file but did not
> succeed yet. Does anyone knows the right procedure to introduce this ions
> into the file ions.itp? do we have to change anything more in order to
> GROMACS recognize the new ion?

The [moleculetype] entries are straightforward.  Just follow the same format. 
The problem is in finding suitable LJ parameters for a new Ag atom type.  Those 
have to be added to ffnonbonded.itp, but it may not be straightforward to derive 
those.  Additive representations of metals are very crude.



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


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