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

Mark Abraham mark.abraham at anu.edu.au
Sat Jun 23 05:20:12 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.

In the absence of a detailed description of what you're doing, it's going
to be hard to convince anyone that the problem resides with GROMACS rather
than your use of it, or your other method you refer to - particularly as
an inexperienced user. I'd suggest developing scripts that do an entire
calculation so that you have some basis for recording exactly what you did
and making it reproducible.

> 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?

The installation guide on the website is fine for the vast majority of
systems. I'm not aware of a test suite per se, because MD is not
reproducible between slightly different hardware. You should be able to
reproduce ensemble averages with accuracy, however.


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