[gmx-users] Generating Entropy from Umbrella Sampling Data

[Billy Williams-Noonan]

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

   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

-- 
Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

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