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.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 02 2015 - 06:00:10 PST
