[gmx-users] Regarding 1-d free energy profile from g_sham
Justin A. Lemkul
jalemkul at vt.edu
Mon Oct 3 15:37:48 CEST 2011
bipin singh wrote:
> Thanks for your reply.
> I have attached two figures here.
> The first figure 1d_fel is, what I am trying to get through g_sham and
> the second figure 1d_fel_sham is what I got from g_sham.
> The bindex.ndx file contains the frame indices for each bins.Now the
> problem is how to transform or determine the
> exact PC's values from these frame indices.
> Please provide your suggestions.
The only thing I can think to do would be to adjust the bin width with g_sham
-bw to try to narrow down which values fall where, but I don't know if that will
negatively impact any of the calculations. In any case, you'll have to
determine which values fall into which bins to make the plot that you want.
This will likely require modifying the g_sham code or some scripting to
post-process the output.
> On Mon, Oct 3, 2011 at 17:45, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
> bipin singh wrote:
> I am using g_sham to plot a one dimensional free energy profile
> for a given reaction coordinate( in my case it is first principal
> component(PC1) from a principal component analysis). It gives me
> the bin index Vs free energy plot, but I want PC's value
> Vs free energy plot. Please suggest me whether it is possible
> through g_sham or not.
> Doubtful. g_sham creates free energy surfaces, which are inherently
> 2D. I don't think you can get it to calculate the free energy of a
> given PC value, although from the free energy vs. bin plot you can
> probably determine something close. The bindex.ndx file should
> contain some information that can be used to translate the bin to
> the values contained within, since it's all derived from a histogram.
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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> Bipin Singh
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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