[gmx-users] WHAM

[Justin A. Lemkul]

Anirban Ghosh wrote:
> Hi Justin,
> 
> Thanks a lot for the reply.
> Yes I have had a look at section 4.4.2. But section 5.3 tells that this 
> WHAM can be used with the REMD data set as well. So my question is that 
> how to present this REMD data of multiple trajectories as input to WHAM? 
> Do I need to work around with the WHAM code or there is some other way?

Also in section 5.3 is the procedure for how to use REMD data, but I don't think 
it will ever accomplish what you want.  The input into WHAM would be energies, 
not RMSD vs. R(g), as you initially stated as your goal.  You can easily build 
free energy surfaces of RMSD vs. R(g) using g_sham, however.

-Justin

> Any suggestion is welcome. Thanks again.
> 
> 
> Regards,
> 
> Anirban
> 
> On Thu, Sep 16, 2010 at 5:28 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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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

========================================