[gmx-users] 100-quartz force field for GROMACS using CGenFF

Justin Lemkul jalemkul at vt.edu
Sun Mar 5 17:14:47 CET 2017

On 3/5/17 6:56 AM, Ivan Gladich wrote:
> Dear all,
> I would like to simulate an alpha-quartz (100) hydroxylated/hydrogenated
> interface using GROAMCS.
> Force field parameters and structure are available in CHARMM
> (http://mackerell.umaryland.edu/charmm_ff.shtml) and  reported in the
> supplemental material of Lopes, P.E.M., Murashov, V., Tazi, M., Demchuk, E. and
> MacKerell, Jr., A.D. "Development of an Empirical Force Field for Silica.
> Application to the Quartz-Water Interface," Journal of Physcial Chemistry B 110:
> 2782-2792, 2006.
> Since I am not familiar with CHARMM force field (and crystal simulations as
> well), my plan was to create the FF in CHARMM and then convert it to GMX
> format.  I copied the quartz (100) structure reported in the paper above,
> converting it in .mol2 format, adding PBC information (see mol2 attached below).
> Then I tried using CHARMM General Force Field (CGenFF) program
> (https://cgenff.paramchem.org) uploading my .mol2 file. If I understand
> correctly, the quartz parameters reported in the paper above should be present
> in CGenFF program. However, I am getting error of the type:
> "Now processing molecule Q100 ... attype warning: element not supported;skipped
> molecule."

The parameters you need are not part of CGenFF at all.  They're CHARMM force 
field parameters and are distinct from CGenFF.  They're in the "silicates" 
subdirectory of the CHARMM toppar files available from the link you quote above.

> Since I read from this mailing list that some of you currently use CGenFF, I
> would like to ask whether some of you have some advise on
> how to get this force field for this structure running in GROAMCS, using CGenFF
> or any other alternative way.

This will require additional force field files (those found in "silicates") to 
be converted to GROMACS format.  Contact me off-list if you need help doing 
this; there are various niche parts of the CHARMM force field that I haven't 
converted simply because no one has needed them and I don't have test cases for 

I don't know anything about such structures, so the subsequent application of 
the parameters is something you'll have to figure out, likely by constructing a 
topology using gmx x2top.



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


More information about the gromacs.org_gmx-users mailing list