Hi,
That is strange.
This looks like a different box size than you mailed yesterday.
Could you mail me the tpr file that caused this error?
Berk
Date: Wed, 19 Nov 2008 14:22:29 +
From: [EMAIL PROTECTED]
Subject: RE: [gmx-users] gromacs 4.0.2 error in continuation to triclinic skew
Hello,
the run didn't even start and I got this:
Initializing Domain Decomposition on 8 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Minimum cell size due to bonded interactions: 1.000 nm
Scaling the initial minimum size with 1/0.8 (option -dds)
0.
In 4.0.0 you communicate twice as many atoms, so 4.0.2 will run faster.
I would suggest to run mdrun -rdd 1 and see if you don't get the missing
interaction errors anymore.
Berk
Date: Wed, 19 Nov 2008 14:06:17 +
From: [EMAIL PROTECTED]
Subject: RE: [gmx-users] gromacs 4.0.2 error in conti
Hello,
thank you for all your responses up to now. The thing is getting much more
clearer.
Yet, as far as the distance is concerned, this is a little bit worrying,
because I have bonded interactions no more than 0.154 nm away. So a distance
more than a whole nm I think that should be very long
dd grid setups).
Berk
Date: Wed, 19 Nov 2008 00:43:48 +
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: [gmx-users] gromacs 4.0.2 error in continuation to triclinic skew
error
Hello,
(I remind you that my initial system is a monoclinic crystal, which is a sub
categorie to
Hello,
(I remind you that my initial system is a monoclinic crystal, which is a sub
categorie to triclinic boxes)
compiling gromacs 4.0.2 with fftw3.2 and having the skew problem, now even in
less steps than before, I face this:
Not all bonded interactions have been properly assigned to the do
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