From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Thu Apr 02 2020 - 16:00:34 CDT
The run command wins, but you should be able to check from the log file of
which one was actually executed. From the NAMD tutorial:
"Now we minimize the system to eliminate bad initial contacts, reinitialize
the velocities to the desired target temperature (since minimization sets
velocities to zero), and run for 100ps. We could accomplish the same thing
with two different NAMD runs using the numsteps and minimization options.
Scripting commands such as those below override numsteps.
minimize 1000 ;# lower potential energy for 1000 steps
reinitvels $temperature ;# since minimization zeros velocities
run 50000 ;# 100ps
Naturally, these are not all of the configuration options accepted by NAMD,
but only a rapid introduction to those you are most likely to encounter.
Documentation for these and many other options can be found in the Users
On Thu, Apr 2, 2020 at 2:21 PM soodabeh ghaffari <soodabehghaffari_at_gmail.com>
> Dear all,
> I generated namd files in charmm-gui. At the end of
> step4_equilibration.inp file,
> There are both numsteps and run. I am not sure which one shows the number
> of steps of equilibration. I attached the file.
> Thank you
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