Re: Parameters for determining run time

From: Richard Overstreet (
Date: Mon Nov 07 2016 - 19:12:59 CST


You need to do some research on what the parameters you are changing do
to the simulation. The integrator time step affects how accurately
system trajectories/forces are calculated. I have never seen someone use
a 10fs time step before usually this is at most 2fs when the rigidbonds
parameter is set to "all". I would recommend reading. "understanding
molecular dynamics simulations" by Daan Frenkel before running any more

On 11/07/2016 05:10 PM, Oscar Bastidas wrote:
> Hello,
> 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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