[gmx-users] WHAM

Justin A. Lemkul jalemkul at vt.edu
Sat Sep 18 19:32:08 CEST 2010

ms wrote:
> Hi Justin,
> On 17/09/10 11:51, Justin A. Lemkul wrote:
>> 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.
> I am wondering: Is there an already-done way, for a REMD set of 
> trajectories, to allow g_sham to extract the surface only from a given 
> temperature, from all replicas?

There's nothing automated that I'm aware of.  The trajectories should be 
ensemble-continuous, so you should be able to conduct whatever analysis you want 
on any particular temperature.  You'll have to construct the .xvg input into 
g_sham though, such that the data represented are in two columns, so 
unfortunately, in the case of RMSD vs. R(g), you have to do additional scripting.


> thanks!
> m.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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