[gmx-users] WHAM

[Justin A. Lemkul]

Anirban Ghosh wrote:
> Hi ALL,
> 
> I have carried out REMD simulation on a protein (20 replicas). Now I 
> want to carry 2D PMF calculation using RMSD and Radius of gyration as 
> the reaction coordinates using Grossfield Lab's WHAM package. For this 
> what should be my input parameters to the WHAM program and in which format?
> Any suggestion in this regard is welcome.

I would suggest you consult the documentation for the program (i.e. the 
Grossfield WHAM manual, section 4.2.2).  I don't know how you intend to pass 
your data to a program that is designed for umbrella sampling, but I suppose 
that's your task.

-Justin

> 
> 
> Regards,
> 
> 
> Anirban
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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