VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri May 08 2009 - 10:17:49 CDT

On Fri, 2009-05-08 at 00:57 -0400, KIRTANA S wrote:

kirtana,

> I need to generate psf file for Gold substrate (111) with sulphur
> atoms it.Should I use CHARMM force field to generate the topology and
> force field parameter file
> Can anybody provide any topology file and force field parameter file
> generated from CHARMM .

to the best of my knowledge, there is no automated way to set
this kind of system up with psfgen. simulating thiols on gold
is a tricky issue, depending on how well you want to have the
interactions near the gold surface represented. so before you
go on to do a simulation that has a potential to be completely
bogus, please let us know a little bit about the kind of study
that you want to do and what kind of analysis you plan to make
etc.. the dynamical surface changes of thiols on gold can be
quite complicated and difficult to simulate or determine
experimentally. a lot of attempts have been made in that direction,
with different levels of success. check out
http://dx.doi.org/10.1126/science.1158532
for one that i was involved in and that also cites a lot of the
relevant literature for further review.

cheers,
   axel. 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.