Parameters for determining run time

From: Oscar Bastidas (
Date: Mon Nov 07 2016 - 16:10:34 CST


I am trying to run a simulation in NAMD for 100 picoseconds but the output
files (*.coor and *.dcd) never show when I execute the simulation for this
simulation time. Is there a range of acceptable values for the simulation
time parameters (timestep, dcdfreq and total number of runs) that if I go
beyond, NAMD will not work? I have successfully run 5 and 10 picosecond
simulations by altering those above three parameters in the *.conf file:

for 5 picoseconds:
Timestep=2 femtosec/step
dcdfreq=250 steps/trajectory snapshot
Total run steps=2500 steps

for 10 picoseconds:
Timestep=2 femtosec/step
dcdfreq=500 steps/trajectory snapshot
Total run steps=5000 steps

Both of these scenarios yield results (*.coor and *.dcd files), but when I
try to do a 100 picosecond simulation according to the following
parameters, I never get my *.coor and *.dcd output files even after waiting
for several days:

for 100 picoseconds:
Timestep=10 femtosec/step
dcdfreq=1000 steps/trajectory snapshot
Total run steps=10000 steps

Is there some formula or heuristic to keep in mind when one wishes to alter
these variables for longer timescales? Is there another variable that I
should alter in the *.conf file in order to run at 100 picoseconds that I
may have missed? Thank you.

Oscar Bastidas, Graduate Student
Department of Chemical and Life Science Engineering
Virginia Commonwealth University

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