[gmx-users] WHAM

ms devicerandom at gmail.com
Sat Sep 18 19:40:14 CEST 2010

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!!


More information about the gromacs.org_gmx-users mailing list