AMBER Archive (2007)

Subject: AMBER: PMEMD and restart files

From: Austin B. Yongye (ayongye_at_chem.uga.edu)
Date: Sat May 12 2007 - 13:21:30 CDT

Dear amber users,
I noticed that PMEMD writes restart files during an MD simulation, then
deletes their contents before writing new restart coordinates again. This
is an issue when a simulation is abruptly terminated when there are no
coordinates in the restart file. In an instance whereby the coordinates of
water molecules are not written in the trajectory file, it becomes really
problematic because the restart file can no longer be generated from the
last frame of the simulation.
I was wondering if/how the pmemd code could be modified so that the
restart file is written as in the sander code.

Austin B. Yongye
Complex Carbohydrate Research Center,
University of Georgia,
315 Riverbend Road,
Athens, GA 30602.
Phone: 706 542 0263

"...then, we learn better in a free spirit of curiosity, than under fear
and compulsion..." -St. Augustine of Hippo
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