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

Groenhof, Gerrit ggroenh at gwdg.de
Tue Sep 22 07:59:32 CEST 2015 

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
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        <CAAUhNntNuEV9cwaEbkZAwXNi=rL6XtNepO3PmFXCL_8iSn9Aig at mail.gmail.com>
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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
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        <CAKTwKgpuqdRh=3DPZ0=jAmbqydTtL5R64mytLmYR03OB9LSSCA at mail.gmail.com>
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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
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> >
> >
>
>
> --
> *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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--
_____________

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>
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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
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--
*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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