[gmx-users] Generating Entropy from Umbrella Sampling Data

Billy Williams-Noonan billy.williams-noonan at monash.edu
Tue Aug 16 16:02:58 CEST 2016 

Hi David,

Yes it's a basic question...  More about my inexperience with Gromacs than
anything (and maybe my chemistry background, not my math background...)

Gmx energy gives an enthalpy against time in the .xvg output, am trying to
translate that to enthalpy against pull distance.

What I had been doing was taking the mean state from each distribution in
the histo.xvg output, matching that up to a corresponding pull distance,
and assuming that the mean enthalpy from gmx energy also matched up to that
pull distance.

Is there a better way?

Best regards,

Billy
On Tuesday, 16 August 2016, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> On 16/08/16 09:28, Billy Williams-Noonan wrote:
>
>> 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?
>>
> Maybe I don't understand the question, but I'd say you just plot the
> potential energy (from the energy file) with error bar for each data point
> and normalize to zero at infinite distance.
>
>>
>>    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.use
>>>>>>>>> r/64417
>>>>>>>>> <http://comments.gmane.org/gmane.science.biology.gromacs.use
>>>>>>>>> r/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
>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>>>> posting!
>>>>>>>>
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>>>>>>>>
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>>>>>>>> or
>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>> 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
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>> posting!
>>>>>>
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>>>>>> * For (un)subscribe requests visit
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>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>> --
>>>> 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 http://www.gromacs.org/
>>>> Support/Mailing_Lists/GMX-Users_List before posting!
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>>>>
>>>>
>>>
>>>
>>> --
>>> Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
>>>
>>> *LinkedIn Profile
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>>> prof-0-sb-preview-primary-button>
>>> **|*   +61420 382 557
>>>
>>> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
>>> Royal Parade, Parkville, 3052
>>>
>>>
>>>
>>
>>
>
> --
> 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

*LinkedIn Profile
<http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
**|*   +61420 382 557

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