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

[Patrick Fuchs]

Hi,
in addition to Mark's remarks, I suggest you to read this recent thread 
we had about fluctuations in dg/dl:
http://www.gromacs.org/pipermail/gmx-users/2007-May/027237.html
Some very useful answers pointed out that there are problems of 
convergence and you need *a lot of sampling* to find the same average 
from one block to the other, even if they are 1ns long. You also might 
need a thorough error analysis of your simulation (follow the thread 
mentioned above). One good way to check if everything works fine in your 
installation would be to try reproducing some published values of free 
energy of hydration on simple molecules.
Cheers,

Patrick

Mark Abraham a écrit :
>> 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.
>
> Mark
>
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-- 
_______________________________________________________
Patrick FUCHS
Equipe de Bioinformatique Genomique et Moleculaire
INSERM U726, Universite Paris 7
Case Courrier 7113
2, place Jussieu, 75251 Paris Cedex 05, FRANCE
Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30
E-mail : Patrick.Fuchs at ebgm.jussieu.fr
Web Site: http://www.ebgm.jussieu.fr/~fuchs