AMBER Archive (2008)

Subject: AMBER: Using restart files

From: Lili Peng (
Date: Tue Feb 26 2008 - 17:36:50 CST

Hi everyone,

This is probably a basic yes/no question, but say you're running an MD
simulation by dividing it into separate jobs (standard procedure). With
each job you get a different restart (.rst) file, each corresponding to a
block of time. I've noticed that the restart file is generated early on
during the simulation, usually before my wall time is up (I usually have it
set to 24 hrs per job). My question is: once you've generated the restart
(.rst) file from that initial simulation can you go use that .rst file and
proceed with the simulation for the next block of time while your initial
simulation is still running? If so, would the data you obtain in your 2nd
simulation correspond to that second block of time? Or would I have to wait
for the 24 hours to be over and then run the second simulation, to obtain
accurate data? This is all assuming that I have multiple nodes at use.


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