From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Tue Oct 25 2005 - 13:12:02 CDT
Hi all,
How does on save the resulting coordinates of a NAMD
minimization in a format to do dynamics?
I have a starting PDB and I want to run 1000 steps of
minimization, save it to a second PDB file and then
run dynamics.
It says in the NAMD manual to use:
"outputname < output PDB file >
Acceptable Values: UNIX filename prefix
Description: At the end of every simulation, NAMD
writes two PDB files, one containing
the final coordinates and another containing the final
velocities of all atoms in the simulation.
This option specifies the file prefix for these two
files. The position coordinates will be saved
to a file named as this prefix with .coor appended.
The velocities will be saved to a file named
as this prefix with .vel appended. For example, if the
prefix specified using this option was
/tmp/output, then the two files would be
/tmp/output.coor and /tmp/output.vel."
However, .coor files are binary files.
So how do I obtain the coordinates?
Richard
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