[gmx-users] Generating Entropy from Umbrella Sampling Data

[Billy Williams-Noonan]

Hi David,

  Thank you for all your responses on here. :)  We'll have to make you an
author if/when this gets published haha.

   Will try to use gmx covar / anaeig at every point but my system has
30,000 atoms so it may not be completely faesible to get an accurate value
for the system (same problem as before).

   Could I simply use gmx energy and get an ensemble average enthalpy for
each point?  Then I can use the Gibbs free energy equation to solve for
entropy.

Billy

On Tuesday, 19 July 2016, David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> 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
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