[gmx-users] parallel run hangs (not crashed)
David van der Spoel
spoel at xray.bmc.uu.se
Tue May 16 21:58:59 CEST 2006
chris.neale at utoronto.ca wrote:
>> Are you sure you want comm_mode = angular ? It seems like you have a
>> periodic system.
> I do have PBC and a quick search indicates that angular is possible with PBC but
> can lead to lincs errors or overlaps when using explicit solvent (although I
> can't find any reasoning. Anyone know of a reference?) Regardless, I have
> switched to linear. Hopefully this is the issue here.
It is not impossible per se, but most likely is not meaningful. It may
also lead to unknown problems when the system is not a single molecule.
Use with care.
>> Are you sure you want to run this system without constraints?
> Do you mean all-bonds instead of h-bonds in order to speed things up? My final
> system will be much smaller, I am currently using a 4X size with inverted
> quadrants 1 and 3 to mimic the P21 asymmetric unit of Dolan Biophys. J. 2002
> during membrane equilibration after protein insertion. If you were not
> referencing speed, I would benifit from some more explanation.
A 2 fs time step may be too much with only hbonds constrained. This
*might* also lead to crashes.
>> If the processes are still there you can kill -HUP them and they should
>> terminate gracefully, writing all files etc.
> Thanks for the tip about the -HUP option. And thanks for the lead on comm_mode,
> that seems to be a likely suspect.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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