[gmx-developers] Fundamental question: Order of visiting/moving
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jul 10 20:11:54 CEST 2015
On 10/07/15 19:45, Raed Khashan 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?
This is not how it works. You may be confusing MD for Monte Carlo.
1) compute the forces on all atoms
2) update velocities
3) update positions
4) go to 1.
>
> --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
> To: gromacs.org_gmx-developers at maillist.sys.kth.se
> 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,
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>> Please reply to the sender that you have received this message in
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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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--
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
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