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

[Tsjerk Wassenaar]

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
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> TEL: (903) 565-5783
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> EMAIL: rkhashan at uttyler.edu
>
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