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.
-Justin
On Mon, Oct 3, 2011 at 17:45, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
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 histogram.
-Justin
--
==============================__==========
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
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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-----------------------
/Regards,/
Bipin Singh
------------------------------------------------------------------------
--
========================================
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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