[gmx-users] Generating Entropy from Umbrella Sampling Data
Billy Williams-Noonan
billy.williams-noonan at monash.edu
Wed Aug 17 03:00:13 CEST 2016
Thank you :)
On 17 August 2016 at 10:57, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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!
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> * 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!
>>>>>>>>>>>>
>>>>>>>>>>>> * 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!
>>>>>>>>>>
>>>>>>>>>> * 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
>>>>>>>
>>>>>>> * 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!
>>>>>
>>>>> * 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.
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>> ==================================================
>>>
>>> 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
>>> /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.
>>>
>>>
>>
>>
>>
> --
> ==================================================
>
> 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
> /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
More information about the gromacs.org_gmx-users
mailing list