Re: xsc information in the dcd file?

From: Gianluca Interlandi (
Date: Thu Dec 16 2004 - 11:25:50 CST

> Currently, the PBC data is written into the DCD if and only if you use the
> DCDunitCell option of NAMD. Recently, I talked with Jim about the idea of
> making this the default behavior in future versions of NAMD.

Yes, this would be a good thing. I was expecting it to be written per
default. As I have log-files I can retrieve the size of my cubic box from
the volume-information. Is there a way to insert the crystal information
into a trajectory after it was written?

Another question: How can I calculate the number of hydrogen bonds between
protein and water? My protein moves partly ouside of the primary box, is
the periodicity taken into account for the computation of the hydrogen

Many thanks,


Gianluca Interlandi
                    +41 (0) 1 635 55 93
                    +41 (0)79 655 73 35

PhD-Student of the Department of Biochemistry
at the University of Zurich Irchel, Switzerland

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