[gmx-users] Preparing a silicon bulk

[Justin Lemkul]

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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================