VMD-L Mailing List

From: Anton Arkhipov (anton_at_ks.uiuc.edu)
Date: Tue Apr 28 2009 - 10:34:04 CDT

Hi,

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

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

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.

Best,

Anton.

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:
>
> 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.