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
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
_______________________________________________________
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 : [EMAIL PROTECTED]
Web Site: http://www.ebgm.jussieu.fr/~fuchs
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
