Re: [AMBER] Fwd: Query regarding umbrella sampling

From: Brian Radak <radak004.umn.edu>
Date: Sun, 13 Jan 2013 12:31:23 -0500

Minhazul,

The standard route to umbrella sampling simulations (as outlined in the
AMBER manual) is to use the nmropt module. A variety of coordinates and
harmonic-like potential forms are available and can be specified in an
additional restraint file (which is referenced in mdin).

Regards,
Brian

On Sat, Jan 12, 2013 at 11:07 AM, minhazul arfeen
<minhazularfeen.gmail.com>wrote:

> Dear Sir,
>
>
> I wish to perform Molecular dynamics simulation using umbrella sampling for
> my target protein-ligand complex, But i am not able to get, how to define
> path and direction of reaction coordinates in the mdin files for the
> simulation runs.
>
> Thanks in advance.
>
> --
> Warm Regards
>
> Minhazul Arfeen
> Ph.D. Scholar
> Department of Medicinal Chemistry.
> National Institute of Pharmaceutical Education And Research.
> Mohali
>
>
>
> --
> Warm Regards
>
> Minhazul Arfeen
> Ph.D. Scholar
> Department of Medicinal Chemistry.
> National Institute of Pharmaceutical Education And Research.
> Mohali
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
================================ Current Address =======================
 Brian Radak                                             :     BioMaPS
Institute for Quantitative Biology
 PhD candidate - York Research Group       :     Rutgers, The State
University of New Jersey
 University of Minnesota - Twin Cities         :     Center for Integrative
Proteomics Room 308
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08854-8066
 radak004.umn.edu                                 :
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Received on Sun Jan 13 2013 - 10:00:03 PST
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