David van der Spoel a écrit :
Stéphane Téletchéa wrote:
I've found out where the problem lie (at least one of ...).
Small reminder: i've tried to setup a system consisting of HIV
protease + one ligand on a water box. I used the excellent protocol
from John E. Kerrigan (Drug-enzyme tutorial) in order to set up my
simulation and encountered some problems with it (basically: Box was
shifted at least 10 times. Please see log-file.).
I add some constructive comments on ways to explore where the problem
was (changing the protocol, including ions into the water to get a
better coupling bath, etc.). Thanks to all of them, even if sometimes
humour is hard to catch by email!
I'm not interested in the system per se (i've done other dynamics
working fine with this protocol) but was rather interested in
providing an updated way of doing a drug-enzyme tutorial with latest
force fields (g45a3, g53a6) and using the latest prodrg (since it
allow the output of g43a1-type atoms, mostly transferable to the
newer ones).
I'll put this on the wiki soon.
I've checked many parameters except one: all-bons vs hbonds.
I do not recall a 'rationale' reason for using the all-bonds parameter
(instead of hbonds where it worked for other dynamics simulations) but
the fact is that if i run all-bonds simulations (whatever the starting
system) with NVT+NPT, i see a crash with the error message like this:
Step 1 Warning: pressure scaling more than 1%, mu: -1.59647e+20
-1.59647e+20 -1.59647e+20
Correcting invalid box:
old box (3x3):
old box[ 0]={-9.82630e+20, 0.00000e+00, -0.00000e+00}
old box[ 1]={ 0.00000e+00, -8.90833e+20, -0.00000e+00}
old box[ 2]={ 0.00000e+00, 0.00000e+00, -1.12456e+21}
new box (3x3):
new box[ 0]={-9.82630e+20, 0.00000e+00, -0.00000e+00}
new box[ 1]={ 0.00000e+00, -8.90833e+20, -0.00000e+00}
new box[ 2]={ 0.00000e+00, 8.90833e+20, -1.12456e+21}
using the *same* protocol (same starting structures, etc) and only
changing all-bonds to h-bonds leads to a 'normal' trajectory (no
error, no warning, no crash).
I remember gromacs 3.3.0 had a problem where pme=4 (that lead to the
3.3.1 rapid release). There are a lot of reports on this mailing-list
with crash/segfaults when using all-bonds, and it seems more when
all-bonds are used instead of h-bonds.
Of course it may come from not completely converged dynamics (my setup
is very rapid, the 4 PR steps last only 100 ps), from not enough
minimsed structures, etc.
Could it be also possible there is a problem while using all-bonds
(even with a 2fs time step) instead of in gromacs, and pme_order was
just hiding it ?
I don't think so. All-bonds with 2 fs should work reliably with both
lincs and shake, provided your system is equilibrated to some extent.
I'm ready to provide again detailed steps i've followed, but on
different systems, including systems coming from a working gromacs run
(for instance a snapshot after 10 ns of production) the problem arises
when i switch from h-bonds to all-bonds.
There are many reports about segfaults in gromacs while using all-bonds
constraints, this was assumed to be related to pme (and gromacs 3.3.1
was released to correct this). I *suppose* this may hide another problem
and pme is not alone the culprit.
I'll try to continue this on bugzilla with input files, procedure on the
wiki (since the procedure in itself works with h-bonds) so we can
decipher where this comes from..
Cheers,
Stéphane
--
Stéphane Téletchéa, PhD. http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901
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