[gmx-users] Generating Entropy from Umbrella Sampling Data

Wed Aug 17 02:28:12 CEST 2016

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.

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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>>>>>>>> * 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!
>>>>>>
>>>>>> * 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.
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>
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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

*LinkedIn Profile
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Monash Institute for Pharmaceutical Sciences ( *MIPS* )
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