[gmx-users] Installation/compilation problem ---v3.3.1

philippe ayala philippe.ayala at gmail.com
Fri Jun 22 22:18:38 CEST 2007

Hi all

I have a silly problem and would welcome any suggestions.  At this point i
suspect that this is a installation or compliation problem.

First, let me say that i am a very unsophiticated user of gromacs.  Please,
bear with me if there is a well known fix for this.
I have installed gromacs following the instructions on the website (settings
for double precision and mpi).  I started using it and everything seems to
work pretty well and I have run a number of jobs, mostly FEP's to
familiarize myself better with Gromacs.  The results i get are in line with
published results.  However, on some runs, the average dg/dl values i get
from the outputfile or from using g_analyze_d are out-of-line with what i
can obtain if i process the data myself.   For example, i get a very
different average values for 2 block-averages of 1ns each compared to the
average over the same 2ns.  I've tried a few things and it looks like the
problem resides with my gromacs binaries.  I can expand on this, if need be.

Before I try reinstalling gromacs, i  would appreciate getting some feedback
on the key settings for a porper gromacs installation and how to check for
potential problems.
Also, is there a set of test-jobs i can run to convince myself  that i
installed gromacs properly and that everything is working properly?

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