Re: Monte Carlo with NAMD

From: Neelanjana Sengupta (
Date: Thu Sep 25 2008 - 06:28:27 CDT

Dear Harish,

Thanks for the reply. I should have been clearer. I basically want to find
the lowest energy conformer (both in vaccuo and in water) of a ~50 residue
peptide. I have pdb coordinates for the peptide, and would like to do a
conformational search, and in principle, be able to pull out the lowest
energy conformers. Of course, the problem is quite complicated, and I was
wondering if anybody has attempted something like this with NAMD.


On Tue, Sep 23, 2008 at 10:08 PM, harish vashisth <
> wrote:

> Dear Neelanjana,
> NAMD, as you know, is a molecular dynamics code and MC
> simulations are altogether different. I have performed MC-docking
> simulations by writing a tcl script which runs under VMD. But, I am not sure
> what you are thinking in terms of MC regarding to whatever conformational
> search you refer? If you can be more explicit about it--people might give
> some more ideas.
> Regards,
> --Harish
> On Tue, Sep 23, 2008 at 11:50 AM, Neelanjana Sengupta <
> > wrote:
>> Dear NAMD community,
>> Has anybody performed a conformational search/Monte-Carlo simulation using
>> NAMD? I did not really find any instances in searching the mailing list, nor
>> did I find any instructions in the manual. It would be great if someone has
>> any idea.
>> Thanks and regards,
>> Neelanjana Sengupta

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