the "firsttimestep" conundrum

From: Himanshu Khandelia (
Date: Sun Mar 19 2006 - 15:20:47 CST


I have read the earlier posts, but am still confused with the firstimestep
parameter. Will really appreciate it if this could be made clear:

If one needs to run, say a 10 ns simulation of a 100000-atom system,
naturally, the entire trajectory cannot be obtained at once. So, one can
write a namd config file to run for say, 100 ps (50000 steps) at a time.
After the first 100 ps are COMPLETE, what should be the firsttimestep
parameter ? 0 or 50020 ? (where 20 is the stepspercycle parameter). If I
am not wrong, then it MUST be 50020, and CANNOT be 0 at all ? If so, why
does the NAMD documentation say that a non-zero value "can" be specified,
rathen than saying that is "must" be specified.

If one starts every next 100 ps with a firsttimestep of 0, can NAMD (or
CHARMM) later recognize the actual timestep of each trajectory, and can
the dcd files be merged accordingly and appropriately ?

Thank you very much for the help and comments,


Himanshu Khandelia

Doctoral Candidate,
Kaznessis Research,
Department of Chemical Engineering and Materials Science,
University of Minnesota

Mailing Address:

499, Walter Library,
117, Pleasant St. SE,
Minneapolis, MN 55455

Phone(o): 612-624-4945

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