Coordinate Output in both binary and ASCII. Or converting binary to ASCII in the command line

From: Hugh Martin (
Date: Mon Mar 02 2009 - 10:09:56 CST


I'm attempting to automatically string together subsequent NAMD SMD
simulations via a script which detects when the previous simulation has
finished, converts and renames files to act as input files for the next
simulation, and then submits the job automatically. In order to do this I
need to convert the pdb output file from an initial simulation into an
SMD.pdb input file for a subsequent simulation (this would be done by a
trivial substitution of a field in the pdb output file). I only wish to use
an ASCII pdb file to refer namd to the SMD atom position; for the
coordinates, velocities and periodic boundaries I need to use binary input
files coor, vel, and xsc. Basically, I need both binary and ASCII forms of
output in order to link two SMD simulations automatically.

This presents a problem, as by using binary input files, NAMD insists on
producing binary output files for restart files and final
coordinate/velocity files (circumventing fields such as "binaryoutput off"
in the .conf file). This makes direct conversion of the output coordinate
file to an ASCII SMD.pdb file non-trivial.

Therefore, if my script, which links the first simulation to the subsequent
simulation, is going to succeed, I need NAMD to either output in both binary
and ASCII fomats (is this possible?), or I need to convert the binary output
into ASCII (.coor to .pdb) using the command line (I know .coor files can be
converted to .pdb files using vmd, however scripted use of VMD windows on
distant machines is not possible to my knowledge).

Any help or ideas would be greatly appreciated.

Many thanks,


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