[gmx-users] Preparing a silicon bulk

Kevin C Chan cchan2242-c at my.cityu.edu.hk
Sun Dec 21 08:52:33 CET 2014

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. 

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"

[ 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].

Thanks in advance,

ukevi at gmx.hk

> On 20 Dec, 2014, at 22:13, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
> -- 
> ==================================================
> 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
> ==================================================
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