RE: restart a simulation

From: Joshua D. Moore (
Date: Mon Apr 03 2006 - 14:17:39 CDT

Hi Lily,
You do not need the .dcd files to restart your simulation. This is your
trajectory. I would suggest moving this file to a new name. When you
restart your simulation, NAMD will move this file to a *dcd.BAK file. The
next time, I think it will be overwritten. So I always move it to a new
file, *dcd.BAK1, *dcd.BAK2, etc.
To restart your simulation, I would suggest to make sure the .coor file is
in ../rotation/. or whatever directory your are saying. Then, check your
old configuration file and make sure that you wrote it in binary. You will
by default unless you have
binaryoutput no
or if you are not using binary restart files you will have
binaryrestart no
Chances are that you are using binary files because this is default and it
is easier.
For binary restart files you should have these lines in your configuration
binCoordinates binarycoordinatefile.coor
binVelocities binaryvelocityfile.vel
extendedSystem extendedsystemfile.xsc
You also need to have
coordinates proteindatabasefile.pdb
This is your ascii input .pdb file. The binary coordinate file only has the
coordinates. To associate atom names it uss the .pdb file. The coordinates
in the .pdb file are ignored (because you have them in the binary file). If
you wanted to use ascii coordinate files, then you will not use
binCoordinates and just Coordiantes.


From: [] On Behalf
Of lily jin
Sent: Monday, April 03, 2006 1:26 PM
Subject: namd-l: restart a simulation

I have all the other files on the cluster machine except the dcd file from
the last run, and I want to restart from the last run. From the configure
file I cannot see the dcd file is loaded, but when I sent the job it gave me
the error messege as:
FATAL ERROR: Error reading binary
even the coor file is there.

do you know if the dcd file generated by the previous simulation is used by
the following restart simulation? Thank you!



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