<p dir="ltr">Hi Ra'ed,</p>
<p dir="ltr">Please keep the subject line of the original mail.</p>
<p dir="ltr">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. </p>
<p dir="ltr">Cheers,</p>
<p dir="ltr">Tsjerk</p>
<div class="gmail_quote">On Jul 10, 2015 6:08 PM, "Raed Khashan" <<a href="mailto:rkhashan@uttyler.edu">rkhashan@uttyler.edu</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Thank you Tsjerk!<br>
<br>
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?<br>
<br>
-- Ra'ed<br>
<br>
<br>
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Today's Topics:<br>
<br>
1. Fundamental question: Order of visiting/moving atoms<br>
(Raed Khashan)<br>
2. Re: Fundamental question: Order of visiting/moving atoms<br>
(Tsjerk Wassenaar)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 10 Jul 2015 15:51:36 +0000<br>
From: Raed Khashan <<a href="mailto:rkhashan@uttyler.edu">rkhashan@uttyler.edu</a>><br>
To: "<a href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se">gromacs.org_gmx-developers@maillist.sys.kth.se</a>"<br>
<<a href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se">gromacs.org_gmx-developers@maillist.sys.kth.se</a>><br>
Subject: [gmx-developers] Fundamental question: Order of<br>
visiting/moving atoms<br>
Message-ID:<br>
<85bcedc5031e483fa79eb995ce54bf1d@Dilbert.uttyler.internal><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Hi everyone,<br>
<br>
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?<br>
<br>
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.<br>
<br>
Thank you!<br>
-- Ra'ed Khashan<br>
<br>
<br>
_________________________<br>
Ra'ed S. Khashan, Ph.D., R.Ph.<br>
Assistant Professor<br>
Department of Pharmaceutical Sciences<br>
Ben and Maytee Fisch College of Pharmacy The University of Texas at Tyler<br>
3900 University Blvd., Tyler, Texas 75799<br>
TEL: <a href="tel:%28903%29%20565-5783" value="+19035655783">(903) 565-5783</a><br>
FAX: <a href="tel:%28903%29%20565-5598" value="+19035655598">(903) 565-5598</a><br>
CELL: <a href="tel:%28903%29%20747-7780" value="+19037477780">(903) 747-7780</a><br>
EMAIL: <a href="mailto:rkhashan@uttyler.edu">rkhashan@uttyler.edu</a><mailto:<a href="mailto:rkhashan@uttyler.edu">rkhashan@uttyler.edu</a>><br>
WEBSITE: <a href="https://www.uttyler.edu/pharmacy/faculty/khashan.php" rel="noreferrer" target="_blank">https://www.uttyler.edu/pharmacy/faculty/khashan.php</a><br>
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------------------------------<br>
<br>
Message: 2<br>
Date: Fri, 10 Jul 2015 17:57:18 +0200<br>
From: Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>
To: Discussion list for GROMACS development<br>
<<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>
Subject: Re: [gmx-developers] Fundamental question: Order of<br>
visiting/moving atoms<br>
Message-ID:<br>
<<a href="mailto:CABzE1SjmOaM72iw_vo%2BAvyPTqAKof7rrZykWPPqxFmLsq_JJQQ@mail.gmail.com">CABzE1SjmOaM72iw_vo+AvyPTqAKof7rrZykWPPqxFmLsq_JJQQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Ra'ed,<br>
<br>
The forces and displacements are calculated using the same configuration.<br>
There is no per-atom/quasi-realtime update. That would be awkward.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
On Jul 10, 2015 5:52 PM, "Raed Khashan" <<a href="mailto:rkhashan@uttyler.edu">rkhashan@uttyler.edu</a>> wrote:<br>
<br>
> Hi everyone,<br>
><br>
><br>
><br>
> In MD simulation, for each atom the forces are calculated, and the<br>
> atom is moved accordingly. Then, we get to the next atom, and so forth<br>
> until all atoms are visited, then we start over. My concern is, by the<br>
> time we get to the last atom, it has waited N*timeStep (e.g., 1000<br>
> atoms * 1 fs) before it can move. Has anyone considered the effect<br>
> this might have on the dynamics<br>
> (trajectory) of the simulation? What if the order of the atoms is reversed?<br>
> Wouldn?t it be more ideal to move all atoms at the same time, using<br>
> forces currently in place, before forces for the new positions are calculated?<br>
><br>
><br>
><br>
> I know that since the time step for a move is very small (1<br>
> femto-second) we can assume that the effect of the move on other atoms<br>
> can be neglected (at room temperature), but has that been<br>
> investigated? This can be important if someone is interested in<br>
> understanding the dynamics of folding or unfolding of a protein, for example.<br>
><br>
><br>
><br>
> Thank you!<br>
><br>
> -- Ra?ed Khashan<br>
><br>
><br>
><br>
><br>
><br>
> *_________________________*<br>
><br>
> *Ra?ed S. Khashan, Ph.D., R.Ph.*<br>
><br>
> Assistant Professor<br>
><br>
> Department of Pharmaceutical Sciences<br>
><br>
> Ben and Maytee Fisch College of Pharmacy<br>
><br>
> The University of Texas at Tyler<br>
><br>
> 3900 University Blvd., Tyler, Texas 75799<br>
><br>
> TEL: <a href="tel:%28903%29%20565-5783" value="+19035655783">(903) 565-5783</a><br>
><br>
> FAX: <a href="tel:%28903%29%20565-5598" value="+19035655598">(903) 565-5598</a><br>
><br>
> CELL: <a href="tel:%28903%29%20747-7780" value="+19037477780">(903) 747-7780</a><br>
><br>
> EMAIL: <a href="mailto:rkhashan@uttyler.edu">rkhashan@uttyler.edu</a><br>
><br>
> WEBSITE: <a href="https://www.uttyler.edu/pharmacy/faculty/khashan.php" rel="noreferrer" target="_blank">https://www.uttyler.edu/pharmacy/faculty/khashan.php</a><br>
><br>
><br>
><br>
> [image: UT_Tyler_Logo]<br>
><br>
><br>
><br>
> CONFIDENTIALITY NOTICE: This E-Mail communication (including<br>
> attachments) is covered by the Electronic Communications Privacy Act<br>
> 18, U.S.C 2510-2521, is confidential and/or legally privileged and is<br>
> protected from disclosure. If you are not the intended recipient, you<br>
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> distribution, copying or use in any way of the contents of this communication is strictly prohibited.<br>
> Please reply to the sender that you have received this message in<br>
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