[gmx-users] Regarding force field for silicon oxide

[David van der Spoel]

Den 2019-11-05 kl. 01:59, skrev Mijiddorj B:
> Dear Prof. David van der Spoel,
> 
> Thank you very much for your reply and sending an amazing work.
> I am sorry for asking further questions. Can you give me an advice to use
> the parameters which were considered in the ref#44 in this work?
> Ref#44 uses the OPLS force field and expresses LJ parameters for the
> contents.
> 

The OPLS files for gromacs 4.6 contain this non-standard addition to 
nonbonded types
This is what was used in my paper and ref 44. Note that there is no 
GROMACS force field, so just refer to this as parameters used in those 
papers.

; Added by DvdS 05/2005 copied from GROMACS force field.
  SI         SI     14   28.08000     0.000       A    3.38550e-01 
2.44704e+00



> Best regards,
> 
> Mijiddorj
> 
> 
>> ------------------------------
>>
>> Message: 4
>> Date: Fri, 1 Nov 2019 17:44:38 +0100
>> From: David van der Spoel <spoel at xray.bmc.uu.se>
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] Regarding force field for silicon oxide
>> Message-ID: <68c1ff39-9979-14ac-a1f9-eb1788be0689 at xray.bmc.uu.se>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>> Den 2019-11-01 kl. 17:07, skrev Mijiddorj B:
>>> I would like to simulate a system which contains a silicon oxide surface
>>> and a polymer. Is it possible to simulate in gromacs?
>>> I thought that GROMOS force field could be applied in this purpose. Is it
>>> right? I am not sure.
>> If you have a potential function that supports it and software to build
>> topologies it works, e.g.:
>>
>> David van der Spoel, Erik J. W. Wensink and Alex C. Hoffmann: Lifting a
>> glass from a wet table: a microscopic picture Langmuir 22 pp. 5666-5672
>> (2006) http://pubs.acs.org/cgi-bin/download.pl?la053284f/X8nx
>>
>> However please do not ask me for the files :)
>>
>>>
>>> Also, is it possible to use InterfaceFF and Charmm force fields for this
>>> system? I mean that the silicon oxide could be treated by InterfaceFF,
>> and
>>> CharmmFF could be applied for polymer structure. Do you have any
>>> experience, please let me advice.
>>>
>>> Thanks for your help.
>>>
>>> Best regards,
>>> Mijiddorj
>>>
>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Head of Department, Cell & Molecular Biology, Uppsala University.
>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>> http://www.icm.uu.se
>>
>>
>> ------------------------------
>>


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se