Re: Parameters for determining run time

From: Vermaas, Joshua (
Date: Mon Nov 07 2016 - 18:43:03 CST

Hi Oscar,

The timestep for minimally restrained atomistic simulations is limited to 2fs, since otherwise the integrator becomes unstable. This is related to the fastest unrestrained degree of freedom in the simulation. If you restrain the bond-lengths to hydrogen, the fastest degree of freedom becomes the heavy-atom bond vibrations, whose period means 2fs is about the maximum. In terms of the dcdfreq, it depends on how much disk space you have, and what you are trying to capture. If you were trying to study water dynamics, I can totally see a small dcdfreq being useful. However, for large-scale interactions, larger dcd frequencies are ok, since your correlation time for those interactions is going to be much longer than the dcd frequency. Personally, I set dcdfreq to save every 2-20ps (1000-10000 steps), depending on how long I intend the simulation to take and what I expect to be important for analysis.


On 11/07/2016 05:19 PM, Richard Overstreet wrote:


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 simulations.

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

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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