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

[Raed Khashan]

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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