I succesfully obtain a restart file, "restart.1". However, when I
compare this to the SANDER-generated restart file, there is a line
missing at the end of the CARNAL-generated file, and this contains the
velocity and box information. All other features appear to be consistent between both files.
Carnal cannot output velocities (1 3-D vector per atom) in a
restrt file. If you have an mdvel, possibly you could treat
it as an mdcrd and have carnal convert to a velocity-only
restrt, which could be manually combined with a 'real' restrt
to produce a restrt-with-velocities.
If there is a box in the mdcrd, and if the prmtop specifies a
box (ifbox>0), then Carnal should put the box info after the
coordinates in the restrt file. If you
% tail mdcrd_file
you should see the box info at the end. See
http://amber.ch.ic.ac.uk/formats.html
for how to check ifbox in the prmtop. Possibly carnal only
outputs x,y,z of the box, without some angles that sander
outputs?
Bill Ross
Received on Tue Sep 25 2001 - 12:32:51 PDT
