<< Setting the simulation time parameters >>

From: I. Camps (icamps_at_gmail.com)
Date: Sat Sep 05 2020 - 13:44:17 CDT

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Dear all,

I am starting to work with NAMD to study small molecules interacting with
proteins.

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
 $outputdcdfile ${output}.dcdxstFile
${output}.xstdcdfreq 50xstFreq
50binaryoutput yesbinaryrestart yesoutputEnergies
     100restartfreq 1000*

*# Multiple timesteppingfirsttimestep 0timestep
1stepspercycle 20nonbondedFreq 2fullElectFrequency
 4*

*# Scriptingminimize 1000reinitvels $temperaturerun
            10000*

[]'s,

Camps

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