AMBER Archive (2009)

Subject: RE: [AMBER] binding free energy

From: Ross Walker (
Date: Sun Mar 01 2009 - 11:29:35 CST

Hi Don,

> It would be nice if sander and pmemd would try to be a little more
> failsafe when writing the restrt file. For example, one could move
> the previous restrt file to a temporary location in the same directory
> (filesystem), write the new restrt, and then, if successful, delete
> the old. Of course, this would cause temporary spikes in disk usage
> that might make failure on a near-full filesystem come sooner rather
> than later. But I think it would be worth it to have failures from
> which one can recover more easily.

Amber 10 can already do something close to this. You just set ntwr<0 and
then every time it writes a restart file it will just append an increasing
number to the end of it. This way you can keep all restart files and you
avoid the problems of corruption happening during a restart write since you
don't overwrite previous restarts so only loose at most the time between the
point of corruption and the previous restart write.

This of course does nothing to help you if you don't have the disk space to
store them all.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
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