Re: Using NAMD for Metropolis Monte Carlo conformational searches

From: Marc Baaden (baaden_at_smplinux.de)
Date: Thu Nov 25 2010 - 06:26:43 CST

Dear Ajasja,

Sorry for replying so late. We have actually encapsulated the IMD
protocol in an easy to use API with some usage examples. One was to
drive a simulation from a script, by injecting forces based on some
analysis of the coordinates. If you're interested in this, you can
either read up on it here [1], or give it a try by downloading it
at [2]. The source code should also contain some comments which might
help to decrypt the IMD protocol.

Hope this helps,
Best wishes,
  Marc

[1] http://dx.doi.org/10.1002/jcc.21235
    Complex molecular assemblies at hand via interactive simulations
    J Comput Chem 30, 2009, 2375-2387

[2] http://mddriver.sourceforge.net

ajasja.ljubetic_at_gmail.com said:
>> But I just remembered the IMD <http://www.ks.uiuc.edu/Research/vmd/
>> imd/>protocol. Perhaps it could be misused for this purpose? It is
>> possible to get the energies back and perhaps using the IMD_FCOORD or
>> IMD_MDCOMM header it is possible to send new conformations. Is there
>> an IMD protokol specification somewhere? I have been reading the
>> example source code found on the "main" IMD site as well as the NAMD
>> source, but it takes longer to get an overview.

>> Best regards, Ajasja

-- 
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden_at_smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217

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