Hi everyone,
As you know, in MD simulation of a biological system, typically, one atom is moved, followed by recalculating forced, then another atom is moved and so forth. Do you know if any of the MD simulation tools, GROMACS, NAMD, AMBER, etc., allows us to run the simulation such that all atoms are moved a single step of the simulation before recalculating forces? There was a study that showed an more accurate results when doing so.
Thank you in advance!
--Ra'ed
no, you made a mistake.
At each time step, all atoms are moving at the same time, not " one after another".
For example, at t=0, forces are calculated for all atoms and atoms move during 0 to 1 timestep. At t = 1, forces are again calculated for all atoms and atoms move during 1 to 2. At t=2, so on...
I don't get what you mean by "as you know" below. (what do we know?)
"As you know, in MD simulation of a biological system, typically, one atom is moved, followed by recalculating forced, then another atom is moved and so forth"
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