[gmx-users] Generating Entropy from Umbrella Sampling Data

Tue Aug 16 09:58:06 CEST 2016

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.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
>>> --
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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
>>
>> 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