I'm not sure about Grossfields package, but I have a demo of 2D PMF (in
dihedral coordinates) from REMD with my WHAM package published this year.
There are example scripts for producing a 2D PMF in dihedral space in
AMBER. Please check the software webpage with all the appropriate links and
the latest version:
https://sites.google.com/site/dansindhikara/Home/software/mr
Let me know if you have any problems with the software.
-Dan
On Fri, Nov 25, 2011 at 2:12 PM, caobb0214 <caobb0214.163.com> wrote:
> dear all,
> I have carried out REMD simulation on a peptide. Now I want to carry 2D
> PMF calculation using RMSD and a specific distance 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.
>
>
>
>
> Regards,
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
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Received on Thu Nov 24 2011 - 22:30:04 PST
