From: I. Camps (icamps_at_gmail.com)
Date: Sat Sep 05 2020 - 13:44:17 CDT
I am starting to work with NAMD to study small molecules interacting with
Using VMD to set-up the simulation, I got the default parameters below.
As the timestep is the default value, 1fs, the simulation runs for 10ps.
My doubt is: which are the recommended values for running a simulation, for
50ns for example, in order to do a quality RMSD, RMSF, etc. analysis?
*# outputset output sim_1UNQ+Lig9369outputname
50binaryoutput yesbinaryrestart yesoutputEnergies
*# Multiple timesteppingfirsttimestep 0timestep
1stepspercycle 20nonbondedFreq 2fullElectFrequency
*# Scriptingminimize 1000reinitvels $temperaturerun
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