AMBER Archive (2009)

Subject: [AMBER] Sander imin=5 option

From: Paul Mortenson (
Date: Tue Jun 16 2009 - 09:46:37 CDT

Dear All,

I've been trying to use sander's imin=5 option for post-processing
trajectories in AMBER 9, with little success. I managed to dig out this
thread on the web:

that seems to suggest that this option is broken, particularly where
PBCs are being used. Has this ever been fixed? Is there another way I
can achieve the same result, or will I have to split the trajectory into
individual restart files and run sander separately on each?

I'm running on CentOS Linux 4.6, just in case that affects anything.

Paul Mortenson

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