[gmx-developers] Fundamental question: Order of visiting/moving
Tsjerk Wassenaar
tsjerkw at gmail.com
Fri Jul 10 20:27:07 CEST 2015
Hi Ra'ed,
No. You start with
for each atom i:
force[i] = forcefield(positions)
displacement[i] = velocity(i, force[i], timestep)
Then:
for each atom i:
position[i] += displacement[i]
Cheers,
Tsjerk
On Jul 10, 2015 7:45 PM, "Raed Khashan" <rkhashan at uttyler.edu> wrote:
> Hi Tsjerk,
>
> I am sorry I did not pay attention to changing the subject line. Hopefully
> this one will do it!
>
> I am still missing something here. Please be patient with me! :)
>
> For N particles, we calculate forces on particle "i" by all other
> particles (N-1), then we displace it. Next we work on particle "i+1", and
> calculate all forces on it by all other (N-1) particles, including particle
> I which we just displaced a step ago. And so forth until we go through all
> particles. By the time we reach the last particle, the forces calculated on
> it will be affected by those particles that have already been displaced. If
> we have started in a reverse order, would we reach the same
> positions/velocities? It is certainly not, thus, the order of the atoms we
> work on will have an effect.
>
> Does that make sense?
>
> --Ra'ed
>
>
>
> -----Original Message-----
> From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se [mailto:
> gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] On Behalf Of
> gromacs.org_gmx-developers-request at maillist.sys.kth.se
> Sent: Friday, July 10, 2015 12:01 PM
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> Subject: gromacs.org_gmx-developers Digest, Vol 135, Issue 10
>
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>
> Today's Topics:
>
> 1. Re: Fundamental question: Order of visiting/moving atoms
> (Raed Khashan)
> 2. Re: Fundamental question: Order of visiting/moving atoms
> (Tsjerk Wassenaar)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 10 Jul 2015 16:44:49 +0000
> From: Raed Khashan <rkhashan at uttyler.edu>
> To: "gromacs.org_gmx-developers at maillist.sys.kth.se"
> <gromacs.org_gmx-developers at maillist.sys.kth.se>
> Subject: Re: [gmx-developers] Fundamental question: Order of
> visiting/moving atoms
> Message-ID:
> <fd68767291c241a9b61a532d6ea9c4cd at Dilbert.uttyler.internal>
> Content-Type: text/plain; charset="us-ascii"
>
> Thank you Mark, and Tsjerk!
>
>
>
> Do you know if the order of the atoms visited has been investigated for
> its effect on the simulation? Or, has the quasi-realtime update been tested
> by others? So I am actually questioning the design principle; has that been
> investigated by others?
>
> --Ra'ed
>
>
>
> _________________________
> Ra'ed S. Khashan, Ph.D., R.Ph.
> Assistant Professor
> Department of Pharmaceutical Sciences
> Ben and Maytee Fisch College of Pharmacy The University of Texas at Tyler
> 3900 University Blvd., Tyler, Texas 75799
> TEL: (903) 565-5783
> FAX: (903) 565-5598
> CELL: (903) 747-7780
> EMAIL: rkhashan at uttyler.edu<mailto:rkhashan at uttyler.edu>
> WEBSITE: https://www.uttyler.edu/pharmacy/faculty/khashan.php
>
> [UT_Tyler_Logo]
>
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> ------------------------------
>
> Message: 2
> Date: Fri, 10 Jul 2015 19:01:14 +0200
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> To: Discussion list for GROMACS development
> <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] Fundamental question: Order of
> visiting/moving atoms
> Message-ID:
> <
> CABzE1Sj1jZvn_QsYjQF-HTgvC-g5GEDh9VZQbCEj57mEBNML0Q at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Ra'ed,
>
> Please keep the subject line of the original mail.
>
> There is no such effect. There can't be such effect. The forces and
> displacement calculated for one particle have no effect on those calculated
> for another.
>
> Cheers,
>
> Tsjerk
> On Jul 10, 2015 6:08 PM, "Raed Khashan" <rkhashan at uttyler.edu> wrote:
>
> > Thank you Tsjerk!
> >
> > Do you know if the order of the atoms visited has been investigated
> > for its effect on the simulation? Or, has the quasi-realtime update
> > been tested by others?
> >
> > -- Ra'ed
> >
> >
> > -----Original Message-----
> > From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se [mailto:
> > gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] On Behalf Of
> > gromacs.org_gmx-developers-request at maillist.sys.kth.se
> > Sent: Friday, July 10, 2015 10:57 AM
> > To: gromacs.org_gmx-developers at maillist.sys.kth.se
> > Subject: gromacs.org_gmx-developers Digest, Vol 135, Issue 7
> >
> > Send gromacs.org_gmx-developers mailing list submissions to
> > gromacs.org_gmx-developers at maillist.sys.kth.se
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developer
> > s
> >
> > or, via email, send a message with subject or body 'help' to
> > gromacs.org_gmx-developers-request at maillist.sys.kth.se
> >
> > You can reach the person managing the list at
> > gromacs.org_gmx-developers-owner at maillist.sys.kth.se
> >
> > When replying, please edit your Subject line so it is more specific
> > than
> > "Re: Contents of gromacs.org_gmx-developers digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Fundamental question: Order of visiting/moving atoms
> > (Raed Khashan)
> > 2. Re: Fundamental question: Order of visiting/moving atoms
> > (Tsjerk Wassenaar)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 10 Jul 2015 15:51:36 +0000
> > From: Raed Khashan <rkhashan at uttyler.edu>
> > To: "gromacs.org_gmx-developers at maillist.sys.kth.se"
> > <gromacs.org_gmx-developers at maillist.sys.kth.se>
> > Subject: [gmx-developers] Fundamental question: Order of
> > visiting/moving atoms
> > Message-ID:
> > <85bcedc5031e483fa79eb995ce54bf1d at Dilbert.uttyler.internal>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > Hi everyone,
> >
> > In MD simulation, for each atom the forces are calculated, and the
> > atom is moved accordingly. Then, we get to the next atom, and so forth
> > until all atoms are visited, then we start over. My concern is, by the
> > time we get to the last atom, it has waited N*timeStep (e.g., 1000
> > atoms * 1 fs) before it can move. Has anyone considered the effect
> > this might have on the dynamics
> > (trajectory) of the simulation? What if the order of the atoms is
> reversed?
> > Wouldn't it be more ideal to move all atoms at the same time, using
> > forces currently in place, before forces for the new positions are
> calculated?
> >
> > I know that since the time step for a move is very small (1
> > femto-second) we can assume that the effect of the move on other atoms
> > can be neglected (at room temperature), but has that been
> > investigated? This can be important if someone is interested in
> > understanding the dynamics of folding or unfolding of a protein, for
> example.
> >
> > Thank you!
> > -- Ra'ed Khashan
> >
> >
> > _________________________
> > Ra'ed S. Khashan, Ph.D., R.Ph.
> > Assistant Professor
> > Department of Pharmaceutical Sciences
> > Ben and Maytee Fisch College of Pharmacy The University of Texas at
> > Tyler
> > 3900 University Blvd., Tyler, Texas 75799
> > TEL: (903) 565-5783
> > FAX: (903) 565-5598
> > CELL: (903) 747-7780
> > EMAIL: rkhashan at uttyler.edu<mailto:rkhashan at uttyler.edu>
> > WEBSITE: https://www.uttyler.edu/pharmacy/faculty/khashan.php
> >
> > [UT_Tyler_Logo]
> >
> > CONFIDENTIALITY NOTICE: This E-Mail communication (including
> > attachments) is covered by the Electronic Communications Privacy Act
> > 18, U.S.C 2510-2521, is confidential and/or legally privileged and is
> > protected from disclosure. If you are not the intended recipient, you
> > are hereby notified that any retention, disclosure, dissemination,
> > distribution, copying or use in any way of the contents of this
> communication is strictly prohibited.
> > Please reply to the sender that you have received this message in
> > error, and then delete it.
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> >
> > ------------------------------
> >
> > Message: 2
> > Date: Fri, 10 Jul 2015 17:57:18 +0200
> > From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> > To: Discussion list for GROMACS development
> > <gmx-developers at gromacs.org>
> > Subject: Re: [gmx-developers] Fundamental question: Order of
> > visiting/moving atoms
> > Message-ID:
> > <
> > CABzE1SjmOaM72iw_vo+AvyPTqAKof7rrZykWPPqxFmLsq_JJQQ at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi Ra'ed,
> >
> > The forces and displacements are calculated using the same configuration.
> > There is no per-atom/quasi-realtime update. That would be awkward.
> >
> > Cheers,
> >
> > Tsjerk
> > On Jul 10, 2015 5:52 PM, "Raed Khashan" <rkhashan at uttyler.edu> wrote:
> >
> > > Hi everyone,
> > >
> > >
> > >
> > > In MD simulation, for each atom the forces are calculated, and the
> > > atom is moved accordingly. Then, we get to the next atom, and so
> > > forth until all atoms are visited, then we start over. My concern
> > > is, by the time we get to the last atom, it has waited N*timeStep
> > > (e.g., 1000 atoms * 1 fs) before it can move. Has anyone considered
> > > the effect this might have on the dynamics
> > > (trajectory) of the simulation? What if the order of the atoms is
> > reversed?
> > > Wouldn?t it be more ideal to move all atoms at the same time, using
> > > forces currently in place, before forces for the new positions are
> > calculated?
> > >
> > >
> > >
> > > I know that since the time step for a move is very small (1
> > > femto-second) we can assume that the effect of the move on other
> > > atoms can be neglected (at room temperature), but has that been
> > > investigated? This can be important if someone is interested in
> > > understanding the dynamics of folding or unfolding of a protein, for
> > example.
> > >
> > >
> > >
> > > Thank you!
> > >
> > > -- Ra?ed Khashan
> > >
> > >
> > >
> > >
> > >
> > > *_________________________*
> > >
> > > *Ra?ed S. Khashan, Ph.D., R.Ph.*
> > >
> > > Assistant Professor
> > >
> > > Department of Pharmaceutical Sciences
> > >
> > > Ben and Maytee Fisch College of Pharmacy
> > >
> > > The University of Texas at Tyler
> > >
> > > 3900 University Blvd., Tyler, Texas 75799
> > >
> > > TEL: (903) 565-5783
> > >
> > > FAX: (903) 565-5598
> > >
> > > CELL: (903) 747-7780
> > >
> > > EMAIL: rkhashan at uttyler.edu
> > >
> > > WEBSITE: https://www.uttyler.edu/pharmacy/faculty/khashan.php
> > >
> > >
> > >
> > > [image: UT_Tyler_Logo]
> > >
> > >
> > >
> > > CONFIDENTIALITY NOTICE: This E-Mail communication (including
> > > attachments) is covered by the Electronic Communications Privacy
> > > Act 18, U.S.C 2510-2521, is confidential and/or legally privileged
> > > and is protected from disclosure. If you are not the intended
> > > recipient, you are hereby notified that any retention, disclosure,
> > > dissemination, distribution, copying or use in any way of the
> > > contents of this
> > communication is strictly prohibited.
> > > Please reply to the sender that you have received this message in
> > > error, and then delete it.
> > >
> > >
> > >
> > >
> > >
> > > --
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