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

[Justin A. Lemkul]

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 <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> 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>
> 
>     ==============================__==========
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/__mailman/listinfo/gmx-users
>     <http://lists.gromacs.org/mailman/listinfo/gmx-users>
>     Please search the archive at
>     http://www.gromacs.org/__Support/Mailing_Lists/Search
>     <http://www.gromacs.org/Support/Mailing_Lists/Search> before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
>     <http://www.gromacs.org/Support/Mailing_Lists>
> 
> 
> 
> 
> -- 
> -----------------------
> /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

========================================