[gmx-developers] Fundamental question: Order of visiting/moving atoms
Raed Khashan
rkhashan at uttyler.edu
Fri Jul 10 18:29:20 CEST 2015
Thank you Mark!
So I am actually questioning the design principle; has that been investigated by others?
--Ra'ed
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Today's Topics:
1. Re: gromacs.org_gmx-developers Digest, Vol 135, Issue 7
(Raed Khashan)
2. Re: Fundamental question: Order of visiting/moving atoms
(Mark Abraham)
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Message: 1
Date: Fri, 10 Jul 2015 16:07:49 +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] gromacs.org_gmx-developers Digest, Vol
135, Issue 7
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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
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Today's Topics:
1. Fundamental question: Order of visiting/moving atoms
(Raed Khashan)
2. Re: Fundamental question: Order of visiting/moving atoms
(Tsjerk Wassenaar)
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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
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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>
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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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>
>
> --
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Message: 2
Date: Fri, 10 Jul 2015 16:15:46 +0000
From: Mark Abraham <mark.j.abraham 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:
<CAMNuMAQ=_a7c_UtSFHh9cV+U9MEKkQsas5pa81qM-x+n6AaCMQ at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi,
Indeed. Force computation is complete before any updates take place, and vice-versa. In future at extreme scales of parallelism, we might have to relax the way we express those semantics in code, but the same design principle applies.
Mark
On Fri, Jul 10, 2015 at 5:57 PM Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 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.
>>
>>
>>
>>
>>
>> --
>> Gromacs Developers mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_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-develope
>> rs or send a mail to gmx-developers-request at gromacs.org.
>>
> --
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