From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Tue Oct 03 2006 - 14:19:10 CDT
NAMD stores the number of steps and not the total simulation time. What
you see "0,100,200... etc." are the number of steps and not the elapsed
time. If you multiply it with 5 fs (your selected time step) you will get
the elapsed time, i.e., 0 fs, 500 fs, 1000 fs ... etc.
The other question is: Are you sure you want to perform your simulation
with such a large time step? In a normal simulation the energy will
diverge. Usually one chooses 1 fs or 2 fs if rigidBonds is on.
Gianluca
On Tue, 3 Oct 2006, santanu chatterjee wrote:
> Hi NAMD users,
> I was running a simulation using NAMD with timestep
> 5 fs and numsteps 5000. I was recording the energies
> once every 100 steps. I thought I will see in my
> output file the energies stored at times 0 fs, 500 fs,
> 1000 fs,...
> But it shows 0,100,200... etc.
>
> I guess NAMD saves only the step number in output
> file. Does it store the total simulation time elapsed
> anywhere? or is there any way one can choose to store
> total simulation time in output file?
>
> Thanks in advance,
> Santanu
>
>
>
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-----------------------------------------------------
Dr. Gianluca Interlandi gianluca_at_u.washington.edu
+1 (206) 685 4435
+1 (206) 714 4303
http://biocroma.unizh.ch/gianluca/
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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