AMBER Archive (2009)

Subject: Re: [AMBER] LINMIN failure notice

From: case (
Date: Fri Sep 18 2009 - 06:38:33 CDT

On Fri, Sep 18, 2009, Jio M wrote:
> but it was suggested to do first minimisation without SHAKE then second
> minimisation with this case I got no error in first
> minimisation  but with SHAKE LINMIN failure again noticed.. what
> is  reason and solution for this .......

There is no solution; you have either turn off shake, or live with the limited
amount of minimization you get with shake turned on.

[If you really need to minimize fully with SHAKE, you can take a look at nab,
which has this capability. But the reason it is not implemented in sander is
that none of the Amber developers ever thought is was enough of an essential
component to implement. To quote the Lord High Executioner, "it won't be


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