Re: newby in NAMD

From: Vermaas, Josh (
Date: Fri May 14 2021 - 12:05:20 CDT

Lots and lots of simulation steps. To generate a nanosecond (or microsecond, or whatever you fancy) trajectory, NAMD calculates the forces experienced by the atoms in their given configuration, and recalculates the positions for the atoms a femtosecond later. It then recalculates the forces, and then recalculates positions again. Doing this two times, the positions now reflect the system 2fs after the start of the simulation. Do this a thousand times, and the simulation reflects 1 picosecond of motion. Do this a million times, and the simulation reflects 1 nanosecond of motion. Do this a billion times, and you get a microsecond worth of trajectory.


On 5/14/21 12:12 PM, joseph pareti wrote:
I have a stupid question, but I need to start somewhere: I read that NAMD can do 'nanoseconds simulations' on some supercomputers, but the time step for atomic movements is in the order of femtoseconds. How can this be done?
Thanks for any insight.

Joseph Pareti - Artificial Intelligence consultant
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