AMBER Archive (2005)

Subject: AMBER: write format of restart crd in sander/pmemd

From: Peter Varnai (pv232_at_cam.ac.uk)
Date: Thu May 19 2005 - 07:12:22 CDT

Dear Amber developers,

I am getting problems more frequently with unwrapped PBC explicit
water simulation that the coordinates get out of bound in the restart
file during the course of long simulations. It is a hassle to write a
new rst file with imaged coordinates with ptraj as it does not write
out velocity information (only zeros). Maybe it is safer to do a
ntpr=1, iwrap=1 sander/pmemd run to write out a wrapped.rst.

If I increase writing/reading from 12.8 (?) to 13.8 will I break
something else? can this be default in the next version of the code?
can ptraj be modified to write out the velocity (and also time)
information?

Thanks,
Peter
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