Restart while runing torsion-angle MD

abonvin at igc.phys.chem.ethz.ch abonvin at igc.phys.chem.ethz.ch
Fri Jun 13 02:03:00 EST 1997


>
>Dear X-PLOR users,
>
>Does anyone know if I can write down a restart file while running
>torsion angle molecular dynamics?

Restarting a torsion MD is somewhat a problem if you want to have a smooth
trajectory. To my knowledge, torsion angle dynamics does not allows for
restart files. The only way would be to save your positions and velocities
to file and re-read them at start (this can be done outside the torsion
statement, or inside it by writing postion and velocities trajectories). 
If you do so, it is important for precision to save them in binary (especially 
for the velocities). I noticed that restarting usually generates a discontinuity 
in your trajectory which is also reflected in your temperature and energies.
This comes I think from the conversion atom-velocities to group-velocities
and there is no good way to avoid it. To minimize that I used to run
one step at restart, check the temperature and calculate a scaling factor
to obtain the proper temperature that I apply to my restart velocities.

Of course, if you use torsion angle MD purely for refinement, non-smooth 
continuation is not really a problem.

Cheers,
Alexandre


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| Dr. Alexandre Bonvin           | Phone: Int+41-1-632-5504              |
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