Re: [AMBER] SHAKEH hydrogen clusters

From: David A Case <>
Date: Thu, 17 Sep 2020 09:24:55 -0400

On Sat, Sep 12, 2020, wrote:

>Here is a small example. It is a prmtop based alchemical scheme where
>the system is simulated with progressively different prmtops to alter
>the geometry of the system. In this case, the intended outcome is to
>"grow" a glycine right after the alanine. The system fails with pmemd,
>but it works perfectly fine with sander. The attached prmtop and
>inpcrd represent the first step of the simulation.

Can you send an mdin file as well as the exact flags you gave to the
programs? If I run a short simulation with with your files, with
either sander or pmemd, I see no errors.


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Received on Thu Sep 17 2020 - 06:30:02 PDT
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