Re: Can someone PLEASE explain the "firsttimestep" parameter ?

From: Brian Bennion (
Date: Wed Mar 22 2006 - 16:43:18 CST


How different are the energies? Depending on the number of processors the
the timing of the sends and receives, the energies are not garuanteed to
be equal between two MD runs at each step. Which version of namd are you

Having said that, the firsttimestep parameter is mostly meaningless to
namd, its a place keeper for us humans that like to organize time.
Set it to what will keep your jobs organized.

Catdcd will run over a lot of errors. Its not checking every data point
for full accuracy instead it looks for the header information given at
each write and skips to the next frame.

Does this help?


On Wed, 22 Mar 2006, Himanshu Khandelia wrote:

> Hello,
> I have been totally baffled with the firsttimestep parameter, and its
> meaning. I ran an equiliration run for 89000 steps. I then started a
> dynamics run, as a continuation of equilibration, varying the
> firsttimestep parameter as follows:
> Case 1: firsttimestep 0
> Case 2: firsttimestep 89000
> Case 3: firstimestep 89020 (20 was the stepspercycle parameter)
> Case 4: I did not define the firsttimestep parameter
> In EACH of the above cases, I get different energies and coordinates.
> Which one is the correct value to use, and why ? Also, in each case,
> "catdcd" merges the dcd files from equilibration and dynamics without any
> errors.
> HELP !
> -Himanshu

   Brian Bennion, Ph.D.
   Biosciences Directorate
   Lawrence Livermore National Laboratory
   P.O. Box 808, L-448
   7000 East Avenue phone: (925) 422-5722
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