AMBER Archive (2003)

Subject: Re: AMBER: The lost velocities in the restart file generated by Ptraj

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Dec 29 2003 - 18:11:54 CST

> The restart file generated from the trajectory file by
> Ptraj lose the information of velocities and all the
> velocities are reset to zero. Is there a way to obtain
> the velocities from the mdvel file and add to the restart
> file, so that, MD simulation can continue?

If you have an mdvel file, you could treat it as if it were
an mdcrd file, feeding it to ptraj or carnal to convert it to
restrt format, then manually append the restrt-format velocities
(leaving out the header) to the coordinate restrt file.

Bill Ross

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