[gmx-users] Generating Entropy from Umbrella Sampling Data

Tue Aug 2 10:15:27 CEST 2016

Yes we've noticed that.  Our error estimates for enthalpy are quite high
compared to the free energies at each umbrella window.

On 2 August 2016 at 17:10, David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> 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
>>>>> --
>>>>> 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
>>> --
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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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-- 
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