[gmx-users] Regarding 1-d free energy profile from g_sham

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 3 14:15:34 CEST 2011

bipin singh wrote:
> Hello,
> 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 



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


More information about the gromacs.org_gmx-users mailing list