[gmx-users] unusually long run required
feenstra at few.vu.nl
Fri Feb 4 07:52:34 CET 2005
Jaimin Shah wrote:
> Dear Dr. Spoel,
> As per you instruction, I set the time step of 0.002 ps in the pr.mdp file
> and nstxout = 250000. That necessitated setting the no. of steps to
> (nstep) to 1250000. Upon mdrunning, I get the message that the run will be
> completed in July 2006. Am I right in doing the settings?
That seems excessively long. 2.5 ns usually takes a few days at most.
What type of system are you simulating, and which hardware do you use?
> However, I thought that if I want a conformation extracted at every 500
> ps, then nstep should be equal to 5. Setting it that way does not give me
> any .trr file.
You want a frame every 500 ps, and have a 0.002 ps per timestep, so:
500 ps / (0.002ps/step) = 250000 steps
Be aware that in this way, for 2.5 ns simulation, you will only get
(2.5ns/500ps)+1 = 6 conformations. Is that what you want?
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