[gmx-users] addition of hydronium ion in simulation box

Catarina A. Carvalheda dos Santos c.a.c.dossantos at dundee.ac.uk
Tue Sep 22 10:28:58 CEST 2015 

Regarding CpHMD methods, I would just like to add that you have, in fact,
several options. In case you are interested, there is a good summary on
subject @
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation.

Regards,

On 22 September 2015 at 06:59, Groenhof, Gerrit <ggroenh at gwdg.de> wrote:

> Hi,
>
> > Hello justin,
> >
> > Thanks, actually I want to study movement of protons along the lenght of
> a
> > water channel.
> >
>
> > What you need is constant-pH MD, which is not natively supported in
> GROMACS.
>
> What Justin says. There is only a 3.3 version that currently supports
> this, which is available at:
>
> http://www.mpibpc.mpg.de/grubmueller/constpH
>
>
> In addition, if you're interested in proton transfer between waters only,
> HYDYN may be an option for you:
>
> http://onlinelibrary.wiley.com/doi/10.1002/jcc.23536/suppinfo
>
> However, from what you describe I assume that protein side chains may be
> involved as well in proton uptake/donation, but we have not yet extended
> HYDYN to include amino acids unfortunately.
>
> Concerning the suggestion by Andre to use DFTB, there is a recent
> implementation in Gromacs by Tomas Kubar:
>
> http://onlinelibrary.wiley.com/doi/10.1002/jcc.24029/abstract
>
>
> Good luck,
>
> Gerrit
>
> -Justin
>
> --
> ==================================================
>
> 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
>
> ==================================================
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 22 Sep 2015 14:22:41 +1200
> From: James Lord <jjamesgreen110 at gmail.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: [gmx-users] force fields selection
> Message-ID:
>         <CAAUhNntNuEV9cwaEbkZAwXNi=
> rL6XtNepO3PmFXCL_8iSn9Aig at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear gmx users,
>
> I want to use either gromos 43a2 or 54a7 in Gromacs to simulate protein
> partitioning at biphasic liquid-liquid interfaces (Similar Justin's
> tutorial for biphasic system). Which one is recommended if anyone has
> experience with such system and why? appreciate any comments? I know 54a7
> is newer version but does it mean it is the best I mean in terms of
> reproducing experimental data etc? or is there any well known problems with
> 43a2 for such a system?
>
> Cheers
> James
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 21 Sep 2015 23:36:27 -0300
> From: Andr? Farias de Moura <moura at ufscar.br>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] addition of hydronium ion in simulation box
> Message-ID:
>         <CAKTwKgpuqdRh=3DPZ0=
> jAmbqydTtL5R64mytLmYR03OB9LSSCA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> It's not H3O+ that diffuses away, it is the H+ that moves from one molecule
> to the next instead.
>
> and protons behave quantum mechanically, so you should not expect any
> classical model to be able to properly describe their dynamics.
>
> for instance, you must consider that a proton may just tunnel from one
> water molecule to the next with an appreciable probability due to the
> combination of small mass, energy barrier height and short distance between
> neighboring water molecules (just like the particle in a square well in the
> standard textbooks of quantum chemistry).
>
> On Mon, Sep 21, 2015 at 10:49 PM, Padmani Sandhu <
> padmanisandhu09 at gmail.com>
> wrote:
>
> > Hello justin,
> >
> > Thanks, actually I want to study movement of protons along the lenght of
> a
> > water channel.
> >
> >
> > Regards,
> >
> >
> > Padmani
> >
> >
> >
> > On Monday, September 21, 2015, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > > [image: Boxbe] <https://www.boxbe.com/overview> This message is
> eligible
> > > for Automatic Cleanup! (jalemkul at vt.edu
> > > <javascript:_e(%7B%7D,'cvml','jalemkul at vt.edu');>) Add cleanup rule
> > > <
> >
> https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Ftoken%3DxOU56wsp8cU%252FlGLCPCIz9Y9c0gcgFshc829PGtYvzGQJtGaD8XdFp84OpXLYG%252FIHACgALfkusLFdfFG2wbL%252B4NIFaq%252B7EL550pZvE9Y9QtzNa2%252Fiqs4JkkEFhMkflbgB8iQQfbKViIA%253D%26key%3Dop2ylYcfXbvcLX0E9YsX3eQVn7HCh5%252FqBBhoMgnGLQ0%253D&tc_serial=22713087415&tc_rand=1639918188&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001
> > >
> > > | More info
> > > <
> >
> http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=22713087415&tc_rand=1639918188&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001
> > >
> > >
> >
> >
> > --
> > *Padmani sandhu*
> > *Research Scholar,*
> > *Center for Computational Biology and Bioinformatics,*
> > *Central University of Himachal Pradesh,*
> > *Temporary Academic Block, Shahpur *
> > *Pin 176206, District Kangra,*
> > *Himachal Pradesh, India*
> > --
> > Gromacs Users mailing list
> >
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>
>
>
> --
> _____________
>
> Prof. Dr. Andr? Farias de Moura
> Department of Chemistry
> Federal University of S?o Carlos
> S?o Carlos - Brazil
> phone: +55-16-3351-8090
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 21 Sep 2015 23:53:22 -0300
> From: Andr? Farias de Moura <moura at ufscar.br>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] addition of hydronium ion in simulation box
> Message-ID:
>         <
> CAKTwKgoek2X4DnV+wgSOS4wmhhj0RcyLeywFiypqt6LsRQ11cQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> for instance, take a look at this reference by Michele Parrinello to see
> some general remarks on how you should proceed if you really want to
> describe the dynamics of protons within a water channel:
>
> http://www.nature.com/nature/journal/v392/n6673/full/392258a0.html
>
> we have already done some simplified simulation for teaching purposes,
> placing a single H3O+ within a water nanodroplet with a few tens of
> (neutral) water molecules, and then performing a short molecular dynamics
> simulation with the semiempirical method MSINDO. the original H3O+ looses
> one of its identical H atoms, which becomes attached to a neighboring H2O
> molecule, which now has 3 identical H atoms, and then looses one of them to
> another neighboring H2O molecule and so on.
>
> I'm still testing it, but DFTB should do the trick as well.
>
> On Mon, Sep 21, 2015 at 11:36 PM, Andr? Farias de Moura <moura at ufscar.br>
> wrote:
>
> > It's not H3O+ that diffuses away, it is the H+ that moves from one
> > molecule to the next instead.
> >
> > and protons behave quantum mechanically, so you should not expect any
> > classical model to be able to properly describe their dynamics.
> >
> > for instance, you must consider that a proton may just tunnel from one
> > water molecule to the next with an appreciable probability due to the
> > combination of small mass, energy barrier height and short distance
> between
> > neighboring water molecules (just like the particle in a square well in
> the
> > standard textbooks of quantum chemistry).
> >
> > On Mon, Sep 21, 2015 at 10:49 PM, Padmani Sandhu <
> > padmanisandhu09 at gmail.com> wrote:
> >
> >> Hello justin,
> >>
> >> Thanks, actually I want to study movement of protons along the lenght
> of a
> >> water channel.
> >>
> >>
> >> Regards,
> >>
> >>
> >> Padmani
> >>
> >>
> >>
> >> On Monday, September 21, 2015, Justin Lemkul <jalemkul at vt.edu> wrote:
> >>
> >> > [image: Boxbe] <https://www.boxbe.com/overview> This message is
> >> eligible
> >> > for Automatic Cleanup! (jalemkul at vt.edu
> >> > <javascript:_e(%7B%7D,'cvml','jalemkul at vt.edu');>) Add cleanup rule
> >> > <
> >>
> https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Ftoken%3DxOU56wsp8cU%252FlGLCPCIz9Y9c0gcgFshc829PGtYvzGQJtGaD8XdFp84OpXLYG%252FIHACgALfkusLFdfFG2wbL%252B4NIFaq%252B7EL550pZvE9Y9QtzNa2%252Fiqs4JkkEFhMkflbgB8iQQfbKViIA%253D%26key%3Dop2ylYcfXbvcLX0E9YsX3eQVn7HCh5%252FqBBhoMgnGLQ0%253D&tc_serial=22713087415&tc_rand=1639918188&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001
> >> >
> >> > | More info
> >> > <
> >>
> http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=22713087415&tc_rand=1639918188&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001
> >> >
> >> >
> >>
> >>
> >> --
> >> *Padmani sandhu*
> >> *Research Scholar,*
> >> *Center for Computational Biology and Bioinformatics,*
> >> *Central University of Himachal Pradesh,*
> >> *Temporary Academic Block, Shahpur *
> >> *Pin 176206, District Kangra,*
> >> *Himachal Pradesh, India*
> >> --
> >> 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.
> >>
> >
> >
> >
> > --
> > _____________
> >
> > Prof. Dr. Andr? Farias de Moura
> > Department of Chemistry
> > Federal University of S?o Carlos
> > S?o Carlos - Brazil
> > phone: +55-16-3351-8090
> >
>
>
>
> --
> _____________
>
> Prof. Dr. Andr? Farias de Moura
> Department of Chemistry
> Federal University of S?o Carlos
> S?o Carlos - Brazil
> phone: +55-16-3351-8090
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 22 Sep 2015 10:14:46 +0530
> From: Padmani Sandhu <padmanisandhu09 at gmail.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] addition of hydronium ion in simulation box
> Message-ID:
>         <CAKot8D66KFB5Xu_ko-B4rUytdy4U2GhepKk=c_kMawLfqWFG=
> A at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Thanks a lot...!!! Actually I was planning to do it with CPMD but I will
> also try the method suggested by you.
>
> On Tuesday, September 22, 2015, Andr? Farias de Moura <moura at ufscar.br>
> wrote:
>
> > [image: Boxbe] <https://www.boxbe.com/overview> This message is eligible
> > for Automatic Cleanup! (moura at ufscar.br
> > <javascript:_e(%7B%7D,'cvml','moura at ufscar.br');>) Add cleanup rule
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> > | More info
> > <
> http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=22719463909&tc_rand=310256639&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001
> >
> >
>
>
> --
> *Padmani sandhu*
> *Research Scholar,*
> *Center for Computational Biology and Bioinformatics,*
> *Central University of Himachal Pradesh,*
> *Temporary Academic Block, Shahpur *
> *Pin 176206, District Kangra,*
> *Himachal Pradesh, India*
>
>
> ------------------------------
>
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-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
School of Life Sciences
University of Dundee
DD1 5EH, Dundee, Scotland, UK

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