On 18/09/10 18:32, Justin A. Lemkul 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.
Ok, very clear, thank you!!
m.
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