[gmx-users] bonded Buckingham interaction

[David van der Spoel]

Frankie Montenegro wrote:
> Well, that's not an option, I am using a modified Morse interaction
> already. That
> was straightforward, I only needed to modify bondfree.c
> But I saw in the manual (after sending the first email) the list of
> files that need to be modified to add a bonded interaction, so I'll
> try that. BTW, it would be much easier to use nonbonded Buckingham: is
> there no way I could set up rvdw at 5A while keeping rcoulomb at 10A?
> Thanks,

what makes you think you can not use Non-bonded Buckingham?

We shouild have the option to have Buckingham pairs though. Please add 
it to the development page of the wiki.

> F.
> 
> On Nov 9, 2007 4:14 AM, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>> Frankie Montenegro wrote:
>>> Hi everyone,
>>>
>>> I am trying to implement a force field for a metalorganic crystal. In this FF,
>>> there is a Buckingham interaction between two neighboring atoms, O and Zn.
>>>  This interaction exists only for atoms on the same crystal site.
>> How about using a Morse potential? It is quite similar.
>> Alt. you can modify the Morse potential.
>>> So, bonded Buckingham interaction added in [ pairs ] would be a
>>> perfect solution.
>>> But reading through the manual, it doesn't appear that bonded
>>> Buckingham is supported
>>>  If this is the case (I'd love to be wrong here), what parts of code
>>> would I have to modify
>>> to make this happen (I hope this doesn't involve any major hacking)?
>>>
>>> Thanks for your help.
>>>
>>> F.
>>>
>>> P.S. I should probably mention, I tried to use nonbonded Buckingham,
>>> cutting it off beyond
>>> a single crystal site, but this doesn't seem possible. My lattice
>>> constant is about 12A,
>>> Coulomb cuttof at 10A, and it seems like there is no suitable combination
>>> of rcoulomb, rlist and rvdw that would cut off Buckingham short of
>>> neighboring site
>>> (while allowing Coulomb to reach that neighboring site).
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://www.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.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>> --
>> David van der Spoel, Ph.D.
>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
>> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.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.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.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.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se