From: Mortimer Hemmit (mortimer.hemmit_at_gmail.com)
Date: Thu Apr 02 2020 - 18:50:12 CDT
As said earlier, the run command overrides the numsteps command. One
difference between them is that "run" runs for ADDITIONAL steps, while
"numsteps" runs just UNTIL that step. This difference will appear if
you use the "firsttimestep" command. For example, if firsttimestep was
run 100 would run ADDITIONAL 100 steps. The simulation would run for
100 steps and end at step 170.
numsteps 100 would run UNTIL 100 steps. The simulation would run for
30 steps and end at step 100.
On Thu, Apr 2, 2020 at 5:49 PM Josh Vermaas <joshua.vermaas_at_gmail.com> wrote:
> 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 Guide"
> On Thu, Apr 2, 2020 at 2:21 PM soodabeh ghaffari <soodabehghaffari_at_gmail.com> wrote:
>> 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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