From: Henri Mone (henriMone_at_gmail.com)
Date: Thu Nov 11 2010 - 19:54:39 CST
Dear Namd users,
My namd simulation hit the wall time limit and stopped before writing
out the *.xsc, *.xst and the *.vel files.
The simulation config file writes out a coordinate trajectory and the
velocity trajectory (option "velDCDfile").
The option "restartfreq" was not used in the namd setup files.
To restart the simulation I only need the last pair of coordinates and
velocities, which I can get from the coordinate trajectory and the
For restarting the simulation following three files are required
*.xsc, *.xst and the *.vel .
The *.xsc file contains only the box information and the last step
nr., creating this file is straight forward. To create the *.xst and
the *.vel file, I extracted the last frame from the coordinates and
the velocity trajectory using "catdcd".
$ catdcd -o prod1.coor -otype namdbin -first 1000 -last 1000 prod1.dcd
$ catdcd -o prodVel1.vel -otype namdbin -first 1000 -last 1000 prodVel1.dcd
When I start the namd simulation with this three files, namd crashes
with following error message:
Command = zcat prod1.vel.Z
Filename.Z = prod1.vel.Z
Command = gzip -d -c prod1.vel.gz
Filename.gz = prod1.vel.gz
FATAL ERROR: Unable to open binary file prod1.vel
What am I doing wrong and how can I create the *.xst and the *.vel file?
Thanks in advance,
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