From: Anton Arkhipov (
Date: Tue Apr 28 2009 - 10:34:04 CDT


Indeed, CG models created with CGTools in VMD can be simulated with
NAMD. Like Axel said, check


and read papers cited there. You'll see that there are two CG models
that you can use (residue-based or shape-based CG), so you will need
to choose one depending on the process you want to study.



On 28 Apr 2009, at 08:32, Axel Kohlmeyer wrote:

> 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:
> 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 http://
> 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.