[gmx-users] Generating Entropy from Umbrella Sampling Data

[David van der Spoel]

On 19/07/16 12:22, Billy Williams-Noonan wrote:
> 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).
You only do this for the biomolecules separately, not the water.
>
>    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.
Yes, this is what we did in the paper :).

>
> 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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>
>


-- 
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