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.
-Justin
thanks!
m.
--
========================================
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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