Hi,
I don't know what the reason for the large LJ14 distance is,
but this will be over 3 bonds, not over 1 bond (which I guess the 0.154 is
that you mentioned).
This has nothing to do with the parallelization.
I would use 4.0.2, since there are many small issues fixed that were in 4.0.0.
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 +0000
From: [EMAIL PROTECTED]
Subject: RE: [gmx-users] gromacs 4.0.2 error in continuation to triclinic skew
error
To: gmx-users@gromacs.org
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 so as to keep this
message to go away. If this has to do with the parallelization, then I might
not worry. Yet, physicaly I think that is a very long distance.
I have to say that the same system worked very nicely with the version 4.0.0
and looking it via ngmx I saw nothing worrying. The properties of my system
where reasonable too.
I insist, because in previous gromacs versions I got similar errors and their
cause was due to running on many processors. The run was crashing, yet running
it only in two
processors I didn't face such problems. It is also curious because in version
4.0.0 I didn't see such an error.
The runs I make take a lot of time, so seeing different error messages at
random makes the post process even more difficult. The 1nm you propose I think
that it is a big distance both for the LJ pairs interactions and of course for
the bonded ones. Also I thought that the table extention was a cut-off for the
LJ pairs interactions, which in my case is 5 nm.
The only thing I can think of for now is to run in less processors...
Thank you,
Regards!
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