Question about optmem input files

From: Carlos Sosa (
Date: Thu Jun 14 2012 - 10:33:50 CDT


In step III, do I need a binary version of the PDB? I only entered
bincoordinates in apoa1.namd but did not touch apoa1.pdb. Yes, I did the
conversion as recommended here.

Info: Running with 1 output processors (1 of them will output

FATAL ERROR: Incorrect atom count in binary file ./apoa1.pdb

CmiAbort is calling on PE:0

aborting job:

FATAL ERROR: Incorrect atom count in binary file ./apoa1.pdb

The compressed psf file will now lie in the directory where the original
psf file is. The name of the new psf file is simply extended with ".inter"

2. Compile and run the memory optimized version

a) compile the NAMD code adding --with-memopt when you run config to create
a build directory

b) modify configuration files:

I. add a field "useCompressedPsf on" in the configuration file, comment the
field "genCompressedPsf" if it exists

II. change the "structure" field to use the newly generated psf file by
simply adding ".inter"

III. obtain a binary format representation of your coordinates. The
coordinate output file of a non memory optimized run would work. Or extract
the binary coordinates using VMD.

IV. replace "coordinates" with "bincoordinates" and replace the reference
to the pdb file with a file containing binary format coordinates.

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