VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Apr 28 2009 - 08:32:24 CDT

On Tue, 2009-04-28 at 15:52 +0800, wuxiao wrote:
> Dear vmd users,
> I find that CGTools Plugin seems very useful in my current study, in
> that I plan to perform CG simulations to achieve a good initial
> configuration for AA simulations to calculate some properties of
> interest. So I wonder if the CG model built from VMD can be used as an
> Input of NAMD,GROMACS and any other MD program. Please give me a "yes"
> or "no" and the reason. Thanks a lot!

dear xiaowu,

do you want somebody to do the simulations and write the papers
for you, too? please give me a "yes" or "no" and the reason. ;-)

but seriously, if an MD code supports the same potential forms
that are needed by the coarse grain model, then in principle it
should be possible to run the same calculations. it is the same
physics, after all. however, since every software uses its own
file format, some conversions and manual labor may be needed.
since GCTools is part of VMD and the NAMD code is maintained by
the same group, you can draw your own conclusion, whether NAMD
would be supported...

other than that, the CGTools has a (for volunteer based open
source code unsually verbose and detailed) documentation at:

http://www.ks.uiuc.edu/Research/vmd/plugins/cgtools/

i suggest you have a close look at the text and the many
references therein

cheers,
   axel.

> best regards,
> xiaowu
>
>
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-- 
=======================================================================
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.