Re: Fixed atoms and dcd file with DCDunitCell on

Date: Sat Jul 23 2005 - 12:11:46 CDT

Hi Joshua,

If you are using *fixed* atoms (i.e., the coordinates don't change at all)
then NAMD will save disk space when writing its DCD files, by only writing
the coords of those atoms once, instead of every frame.

But I think you may be getting confused... "rigidbonds" is a restraint, which
insures that the bond lengths between hydrogens and heavy atoms are held near
their ideal lengths -- eliminating the need for very small timesteps to track
what would otherwise be very fast motion of those light H atoms. But this is
completely distinct from the case where one specifies some atoms to be fixed
in space.

hopefully helpful,

C. Erik Nordgren, Ph.D.
Department of Chemistry
University of Pennsylvania

Quoting "Joshua D. Moore" <>:

> I have noticed that the charmm formatted dcd file (with "DCDUnitCell on")
> includes an extra line giving the atom numbers for all of the free atoms.
> I am using "rigidBonds water". However, this line for the free atoms does
> not seem to appear in my DCD files. Does NAMD not write this line? Or
> does this mean my waters are not fixed?
> Thanks
> Joshua Moore

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