Re: [AMBER] 2-d PMF calculation with REMD

From: Yong Duan <duan.ucdavis.edu>
Date: Fri, 25 Nov 2011 10:40:07 -0800

Just be careful that the energies reported in mdout do not necessarily in
synch with mdcrd in some cases. This may introduce additional error,
particularly when you want to calculate the PMF at a temperature different
than the one of the simulation.

--
yong
On 11/24/11 9:12 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,
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Received on Fri Nov 25 2011 - 11:00:03 PST