[gmx-users] Generating Entropy from Umbrella Sampling Data

[David van der Spoel]

On 19/07/16 09:47, Billy Williams-Noonan wrote:
> Hi All,
>
>    I have seen papers where enthalpy and entropy are plotted against the
> distance of a steered MD pull and am wanting to do something similar.
>
>    I have run a steered MD simulation pulling a cyclic peptide out of the
> binding site and the PMF calculation with *gmx wham* was in reasonable
> agreement with experiment.  to
We have published stuff like that (e.g. J. Chem. Theor. Comput. 9 pp. 
4542-4551 (2013)http://pubs.acs.org/doi/abs/10.1021/ct400404q)
There are two main ways of doing this, rerunning the PMF at different 
temperatures and using the Van 't Hoff equation, or computing the 
entropy (approximately) using gmx covar / gmx anaeig for each of the 
species.

gmx sham is just for plotting an energy landscape, e.g.
J. Mol. Biol. 354 pp. 173-183 (2005)


>
>    What I would like now is plot the entropy and enthalpy components
> against the pull distance.  I stumbled across *gmx sham* and would like to
> use that, however I can't find any information on how to use it online.  I
> found these posts on online forums but have found them to be unhelpful (I'm
> sure it makes sense, it's just I am more of a chemist than a mathematician).
>
> *http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/hmlPKJSt/how-to-use-g-sham
> <http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/hmlPKJSt/how-to-use-g-sham>*
>
> *http://comments.gmane.org/gmane.science.biology.gromacs.user/64417
> <http://comments.gmane.org/gmane.science.biology.gromacs.user/64417>*
>
>    I have also looked through the Gromacs 5.1.2 manual and cannot find
> anything on *gmx sham*.
>
> *http://manual.gromacs.org/documentation/5.1.2/manual-5.1.2.pdf
> <http://manual.gromacs.org/documentation/5.1.2/manual-5.1.2.pdf>*
>
>    Could someone please let me know the exact commands I need to use with *gmx
> sham i*n order to plot entropy and enthalpy against the pull distance?
>
>    Kind regards,
>
> Billy
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se