[gmx-users] gromacs 4.0.2 error in continuation to triclinic skew error
lastexile7gr at yahoo.de
Wed Nov 19 15:06:17 CET 2008
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...
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