Re: [AMBER] Fwd: Regarding QM/MM calculation in AMBER14

From: David A Case <>
Date: Mon, 2 Nov 2015 08:51:27 -0500

On Mon, Nov 02, 2015, Sivanandam M wrote:

> I got the following error, at the time of
> running QM/MM calculation of protein -ligand complex. I dont know what is
> the solution of that problem. the error is.
> *Sum of charges from parm topology file = -2.99899913*
> *Assuming uniform neutralizing plasma*
> *Running AMBER/MPI version on 40 nodes*
> *| WARNING: The number of processors is not a power of 2*
> *| this may be inefficient on some systems.*

As others have noted, these are not errors. However, running QM/MM on 40
nodes (or in parallel at all) is only helpful in very special cases. I
recommend just using the serial version at first. Later, you can
carefully investigate if increasing the number of MPI threads actually
provides a timing advantage.


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Received on Mon Nov 02 2015 - 06:00:10 PST
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