<div dir="ltr">Hi,<div><br></div><div>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.</div><div><br></div><div>Mark</div></div><br><div class="gmail_quote"><div dir="ltr">On Fri, Jul 10, 2015 at 5:57 PM Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Hi Ra'ed,</p>
<p dir="ltr">The forces and displacements are calculated using the same configuration. There is no per-atom/quasi-realtime update. That would be awkward.</p>
<p dir="ltr">Cheers,</p>
<p dir="ltr">Tsjerk</p>
<div class="gmail_quote">On Jul 10, 2015 5:52 PM, "Raed Khashan" <<a href="mailto:rkhashan@uttyler.edu" target="_blank">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">
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<div>
<p class="MsoNormal">Hi everyone,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">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?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">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.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thank you!<u></u><u></u></p>
<p class="MsoNormal"> -- Ra’ed Khashan<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span style="color:#212121"> </span><u></u><u></u></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">_________________________</span></b><u></u><u></u></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">Ra’ed S. Khashan, Ph.D., R.Ph.</span></b><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black">Assistant Professor</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black">Department of Pharmaceutical Sciences</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black">The University of Texas at Tyler</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black">3900 University Blvd., Tyler, Texas 75799 </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black">TEL: <a href="tel:%28903%29%20565-5783" value="+19035655783" target="_blank">(903) 565-5783</a></span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black">FAX: <a href="tel:%28903%29%20565-5598" value="+19035655598" target="_blank">(903) 565-5598</a></span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black">CELL: <a href="tel:%28903%29%20747-7780" value="+19037477780" target="_blank">(903) 747-7780</a></span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black">EMAIL: </span><span style="font-size:10.5pt"><a href="mailto:rkhashan@uttyler.edu" target="_blank"><span style="color:#0563c1">rkhashan@uttyler.edu</span></a></span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black">WEBSITE: <a href="https://www.uttyler.edu/pharmacy/faculty/khashan.php" target="_blank">
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