Re: Monte Carlo with NAMD

From: L. Michel Espinoza-Fonseca (
Date: Thu Sep 25 2008 - 07:28:15 CDT

Dear Neelanjana,

In principle you could be able to perform simulated annealing with
NAMD, and then extract the conformations with the lowest energy. The
problem here is that you might need to apply some restraints (i.e.,
derived from NMR or EPR, if available) in order to get meaningful
results. The other issue you might face is incomplete sampling, as
simulated annealing requires a relative long cooling time.


On Thu, Sep 25, 2008 at 1:28 PM, Neelanjana Sengupta
<> wrote:
> 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.
> Thanks,
> Neelanjana
> 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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