AMBER Archive (2001)

Subject: Re: Velocity information in CARNAL generated restart files

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Sep 25 2001 - 14:32:51 CDT

        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://www.amber.ucsf.edu/amber/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