Hi,
As far as I know, you must build the structure file by yourself, and the
topology file. For the force field, the SiO2 have been included in the
ffG53a6 and opls force field. However, it seems that the LJ parameters
of Si in both of them is inconsistent with the original publication.
regards,
Baofu Qiao
Justin A. Lemkul wrote:
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.
-Justin
Arden Perkins
On Tue, Jan 12, 2010 at 3:23 AM, Batistakis, C. <[email protected]
<mailto:[email protected]>> 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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