AMBER Archive (2008)

Subject: Re: AMBER: PKa calculation

From: David A. Case (
Date: Tue Feb 12 2008 - 11:15:55 CST

On Tue, Feb 12, 2008, Wang, Xuelin wrote:
> set MPIRUN="pam -g 1 mpichp4_wrapper"

I'm not familiar with this syntax, but you need to make sure that you are
asking for the correct number of processes.

> $MPIRUN $AMBER9 -ng 2 -groupfile d2c_groupfile.1

> Error: specified more groups ( 2 ) than the number of processors (
> 1 ) !

This is pretty clear: the system thinks you only asked for one process, but
you need at least as many processes as groups. So, check your MPIRUN setting.


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