[AMBER] MD simulation in gas phase-AMBER 10

From: Dian Jiao <oscarjiao.gmail.com>
Date: Thu, 25 Mar 2010 11:30:45 -0600


I was trying to run simulation for a small molecule (less than 10 atoms) in
gas phase. I generated the prmtop and inpcrd with leap. If I soak it in a
waterbox, the simulation runs perfectly well. However I can't run it with
the molecule in gas phase. Even if it's a simple minimization run
(imin=1,maxcyc=500), it won't do it.

After I launch the job, it only generates a blank mdout, but no mdcrd or
restrt file. The job lasts forever and never stops unless it's killed. No
error message.

But if I add the box dimensions at the bottom of the inpcrd file and run it,
it stops immediately right after it prints out the first step in the mdout
file. Again, no error.

Does anyone know what is wrong and how to run a gas-phase simulation?

Thanks in advance.

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Received on Thu Mar 25 2010 - 11:00:03 PDT
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