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

[Mark Abraham]

Hi,

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.

Mark

On Fri, Jul 10, 2015 at 5:57 PM Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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
>>
>> TEL: (903) 565-5783
>>
>> FAX: (903) 565-5598
>>
>> CELL: (903) 747-7780
>>
>> EMAIL: rkhashan at uttyler.edu
>>
>> WEBSITE: https://www.uttyler.edu/pharmacy/faculty/khashan.php
>>
>>
>>
>> [image: UT_Tyler_Logo]
>>
>>
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