[gmx-users] Preparing a silicon bulk

Justin Lemkul jalemkul at vt.edu
Sat Dec 20 15:13:56 CET 2014

On 12/20/14 5:29 AM, Kevin C Chan wrote:
> Thanks for the reply.
> In principle that is what I plan to do - generate a basic topology (with
> homogeneous charge information) and then manually (or a script) change the
> charge of each SI atom. Honestly I only have experience of writing a simple
> topology for a MARTINI system. So what I expect was first to include the
> gromos forcefield so I have the [defaults] [atomtypes] [bondtypes] defined
> and then manually write the [moleculetypes] and [atoms] in which I can define
> the charges (I assume it will overwrite the charge value defined in
> [atomtypes], right?) then the tens or hundreds of rows of entries were
> treated as one single molecule and finally the [system] and [molecules].

The charge values in ffnonbonded.itp are never used for anything; they're an 
artifact of old intentions.

> However I am now stuck at the step that it seems no forcefield provided by
> Gromacs gives bonded parameters for Si-Si so g_x2top could not work out. Or
> maybe I should give up g_x2top and just manually write the [bondtypes]
> according some parameters provided by the literature and combined with
> nonbonded parameters provided by gromos forcefield, for instance, but this
> then arises the consistency problem Oh god :(

Find a suitable force field in the literature, something that you can use to 
reproduce their findings; implement it (something like an Si or silica surface 
should be very easy, given the few parameters that are needed) and test that you 
can make a sane topology.  Then do your hacks and see how things go.  I don't 
know what kind of validation you'd need to do, and you haven't said by how much, 
or why, the charges will vary across the surface, so that's also hard to say. 
Welcome to the delightful world of force field parametrization :)



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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