[gmx-users] Generating Entropy from Umbrella Sampling Data

Tue Aug 16 09:28:07 CEST 2016

Hi David,

   I was wondering if you had any advice on how to plot enthalpy against
COM pulling distance in the same manner that you have in *Figure 4* above?

   Best regards,

Billy

On 2 August 2016 at 18:15, Billy Williams-Noonan <
billy.williams-noonan at monash.edu> wrote:

> 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
>>>>>>
>>>>>> * Please search the archive at
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>>>>>> posting!
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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
>> --
>> Gromacs Users mailing list
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>
>
>
> --
> Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
>
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>
>

-- 
Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

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