[gmx-developers] Fundamental question: Order of visiting/moving atoms

Raed Khashan rkhashan at uttyler.edu
Fri Jul 10 17:51:49 CEST 2015

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


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.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20150710/f6817485/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.png
Type: image/png
Size: 5616 bytes
Desc: image001.png
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20150710/f6817485/attachment.png>

More information about the gromacs.org_gmx-developers mailing list