[gmx-users] Generating Entropy from Umbrella Sampling Data

Tue Aug 2 09:10:08 CEST 2016

On 20/07/16 02:51, Billy Williams-Noonan wrote:
> 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.
Yes indeed.

The only problem is that enthalpies converge much more slowly than free 
energies.
>
> 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
>> --
>> Gromacs Users mailing list
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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