Re: [AMBER] problem with gas-phase MD simulation in Amber8.

From: Mengjuei Hsieh <>
Date: Fri, 18 Mar 2011 05:19:49 -0700

2011/3/18 marta wiśniewska. <>:
>  I was trying to run simulation for a small arrangement of two molecules (26 atoms) in
>  gas phase. I generated the prmtop and inpcrd with leap. If I soak it in a
>  ACN , solvatebox, the simulation runs perfectly well. However I can't run it with
>  the molecule in gas phase.
[detail snipped]
>  when I run this, job is killed.


Before people looking into the problem, can you provide us some more
details about how your computation got stopped? Is it "killed" by a
job scheduler like sun grid engine, or openpbs, or just by the
operating system? Is there any error message inside the mdout file
(the filename you specified after the "-o")?

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Received on Fri Mar 18 2011 - 05:30:04 PDT
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