[gmx-users] SiO2 simulation

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 12 18:09:56 CET 2010

Arden Perkins wrote:
> I believe pdb files (protein data bank) are only for peptides, so unless 
> you are simulating a peptide you will not need any pdb files for your 

There are numerous utilities that generate .pdb files; it is not true to say 
that .pdb files only contain proteins/peptides.  A .pdb file is simply a 
coordinate format; it can contain anything.

> SiO2. Your structure file (.gro) for SiO2 may be in the fftw library 
> files (or whatever forcefield you're using). Hope that helps.

What do you mean by this?  FFTW has nothing to do with force fields or 
structures of any sort.  And certainly none of the force fields distributed with 
Gromacs will topologies for SiO2, since they are primarily biomolecular.  They 
may contain atom types related to SiO2, however, but probably not pre-built 
topologies, and certainly not coordinate files.


> Arden Perkins
> On Tue, Jan 12, 2010 at 3:23 AM, Batistakis, C. <c.batistakis at tue.nl 
> <mailto:c.batistakis at tue.nl>> wrote:
>     Dear all
>     I am a new user of Gromacs. I am interested to simulate amorphous
>     SiO_2 and I would like to know if someone can send me the .pdb and
>     .top files.
>     Thanks in advance
>     Chrysostomos
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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