Re: [AMBER] MD simulation in gas phase-AMBER 10

From: Carlos Simmerling <>
Date: Thu, 25 Mar 2010 13:34:55 -0400

can you share your input file, and let us know which options you picked to
run it in gas phase? this isn't automatic, the defaults assume a periodic

On Thu, Mar 25, 2010 at 1:30 PM, Dian Jiao <> wrote:

> Hi,
> 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.
> Dian
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Received on Thu Mar 25 2010 - 11:00:04 PDT
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