[gmx-users] SiO2 simulation

[Baofu Qiao]

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. <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
>>
>>
>>     --
>>     gmx-users mailing list    gmx-users at gromacs.org
>>     <mailto:gmx-users at gromacs.org>
>>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>>     Please search the archive at http://www.gromacs.org/search before
>>     posting!
>>     Please don't post (un)subscribe requests to the list. Use the
>>     www interface or send it to gmx-users-request at gromacs.org
>>     <mailto:gmx-users-request at gromacs.org>.
>>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>