Re: time step and total simulation time in conf file

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Sep 14 2011 - 10:53:43 CDT

Hello, Insert Name Here!

Your simulation is fine. DCD files do not contain any info about the
time step duration, so VegaZZ is just taking a guess - that is, it is
"guessing" that 1 fs is a pretty common value for a time step, so why
bother.

Cheers,
the dis-organizer

On 14 September 2011 16:41, Namd Namd <namd_10_at_yahoo.com> wrote:
> Dear namd people,
> I’m confused about assigning the time step  and total simulation time into
> conf file. I wanted to run a simulation for 3.5 ns  with 0.5 fs time step
> and 3500 frame. I think the total simulation time = time step*run .  So I
> wrote a conf file like
>
> firsttimestep      0
> timestep           0.5
> restartfreq        2000 # every 1 ps
> dcdfreq            2000
> xstFreq            2000
> outputEnergies     2000
> outputPressure     2000
> outputtiming       2000
> run 7000000
>
> Then I opened my psf file with vegazz , chose calculate/analysis and loaded
> dcd file and saw that
> Information:
> Start time : 2 ps
> Simulation time : 7000 ps
> Time step : 2000 fs
> Frames : 3500
> These are different with my time step  and total simulation time. What is
> the reason for this ? Is my conf file wrong ? Could you please help me the
> learn assigning the time step  and total simulation time ?
>
> Thank you all for the responses.

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