[gmx-users] Generating Entropy from Umbrella Sampling Data

[Billy Williams-Noonan]

Hi David,

  Thank you...!  To clarify, in Figure 4 of the paper referred to, you seem
to have plotted the enthalpy of each frame against the COM pull distance
and then used those values and the PMFs at each point to compute -TdS ?  If
so I might do something similar.

Billy

On Wednesday, 20 July 2016, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> 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
> --
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