[gmx-users] Preparing a silicon bulk
jalemkul at vt.edu
Sun Dec 21 20:02:37 CET 2014
On 12/21/14 2:52 AM, Kevin C Chan wrote:
> Thanks for the reply.
> I am quite new to the field of Materials so I do need someone else to find a
> “good” paper on parameters for a silicon surface. While I am waiting to for
> that, I am actually very curious that why gromos does not have such
> parameters and nearly all popular forcefields (for biomolecule simulations)
> contains silica parameters. It is strange that we even have Si-Si nonbonded
> parameters in gromos but no bonded ones.
Force fields arise because of what the developers need to do or find value in
constructing. For whatever reasons, they did not deem Si-Si bonded parameters
necessary. There are parameters for other silicon-based materials. It is not
unusual that there are nonbonded parameters for Si-Si interactions but not
bonded, because the materials they parametrized needed such interactions, but
there were no Si-Si bonds.
> In practice, it is also hard to say how my charges vary across the surface
> (they are just 0.X in difference). Basically I am thinking if I could
> generate a topology for a simple silicon bulk then I would just rewrite the
> [atoms] in [moleculetypes] to assign the charges. Like the follows:
> [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1
> 1 no 1.0 1.0
> [ atomtypes ] ;name at.num mass charge ptype c6
> c12 SI 1 28.08 0.000 A 1.000 1.000
> [ bondtypes ] ;i j func b0 kb SI SI 1 1.000 1.000
> #include "gromos54a7.ff/forcefield.itp"
This will cause a fatal error. The forcefield.itp file declares a [defaults]
directive (master information for the force field), so you will get a fatal
error from grompp. See Chapter 5. It is likely better to create a small custom
force field rather than shoehorning something into working.
> [ moleculetype ] ; molname nrexcl SIB 4
> [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 SI
> 1 SIB SI 1 -0.10 2 SI 1 SIB SI 2
> 0.60 3 SI 1 SIB SI 3 -0.30 4 SI 1
> SIB SI 4 -0.20
> [ system ] SIB in Water
> [ molecules ] SIB 1
> In this way what I have to do is to plug correct numbers into [bondtypes].
As stated above, given the finite number of parameters you need, it's better to
just create a small, custom force field in this case.
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