[gmx-users] Generating Entropy from Umbrella Sampling Data

Justin Lemkul jalemkul at vt.edu
Wed Aug 17 02:57:37 CEST 2016 


On 8/16/16 8:55 PM, Billy Williams-Noonan wrote:
> Justin,
>
> Does *gmx distance* plot the distance between the COM of two index groups?
>

It will do whatever you specify (examples on gromacs.org) but yes, it does 
exactly this.

-Justin

> Billy
>
> On 17 August 2016 at 10:50, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 8/16/16 8:28 PM, Billy Williams-Noonan wrote:
>>
>>> Thank you that is what I have been doing... :)
>>>
>>> My problem is that I don't have the average COM distance for each
>>> simulation.  Yes I specify what distance I want in the .mdp settings, but
>>> in the earlier umbrella windows our average COM distance deviates somewhat
>>> from the distance set in the mdp settings.  So I need a reliable way of
>>> getting an average COM distance to match the average energy output from
>>> gmx
>>> energy.
>>>
>>>
>> This is the primary function of gmx distance.
>>
>> -Justin
>>
>>
>> Best,
>>>
>>> Billy
>>>
>>>
>>>
>>> On 17 August 2016 at 00:28, David van der Spoel <spoel at xray.bmc.uu.se>
>>> wrote:
>>>
>>> On 16/08/16 16:02, Billy Williams-Noonan wrote:
>>>>
>>>> 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?
>>>>>
>>>>> You want to average over all conformations in the simulation, same as
>>>> you
>>>> do in the PMF. So for each distance you compute the average energy with
>>>> gmx
>>>> energy and plot it.
>>>>
>>>>
>>>> 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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>>>>>>>>>>>>>
>>>>>>>>>>>>> * For (un)subscribe requests visit
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>>>>>>>>>>>>> -users
>>>>>>>>>>>>> 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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>>>>>>>>>>>
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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
>>>>>>>>>
>>>>>>>>> * 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.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> --
>>>>>>>> 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
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>>
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>
>>>>>> * For (un)subscribe requests visit
>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users 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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>>>>
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>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>>
>>>
>>>
>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
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>>
>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================

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