AMBER Archive (2009)

Subject: Re: [AMBER] Sander imin=5 option

From: Carlos Simmerling (
Date: Tue Jun 16 2009 - 09:50:43 CDT

are you up to date with all patches? if yes, forward your sander script and
mdin, as well as any errors in the mdout. also tell us what amber version
you are using.

On Tue, Jun 16, 2009 at 10:46 AM, Paul Mortenson <> wrote:

> 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.
> Thanks,
> Paul Mortenson
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