Re: [AMBER] Problem about "Too many dipole_dipole interactions for allocated" when heat

From: David A Case <>
Date: Wed, 29 Oct 2014 07:38:52 -0400

On Wed, Oct 29, 2014, Ya Gao wrote:
> I performed a MD simulation under amoeba force field with pmemd.amoeba.MPI
> in amber14.
> The minimization terminates normally. However, when the heat simulation
> reached 9.0 ps, it was interrupted with the message " Too many
> dipole_dipole interactions for allocated".

I haven't seen this in a long time. How big is your system? What is the
value of size_dipole_dipole_list (printed in the mdout file)? It seems quite
odd that your temperature is still less than 2 K after 9 ps of simulation.
Have you run other systems with amoeba?

Since you have a trajectory with snapshots every 500 steps, I'd suggest first
looking at that to see what is going on. A second step is to run a
simulation with the serial version of pmemd.amoeba, to see if this might have
something to do with the MPI code.

Another thing to do is to Google "amber Too many dipole_dipole
interactions for allocated", and try increasing the "safety" parameter as
described there.

If those steps don't help, you will probably have to post files that would
allow someone else to reproduce the problem.


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Received on Wed Oct 29 2014 - 05:00:03 PDT
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