[gmx-users] WHAM

[Anirban Ghosh]

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?
Any suggestion is welcome. Thanks again.


Regards,

Anirban

On Thu, Sep 16, 2010 at 5:28 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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