[gmx-users] error in a parallel job
feenstra at chem.vu.nl
Tue Nov 18 09:15:04 CET 2003
> On Sat, 2003-11-15 at 04:14, Lanyuan Lu wrote:
>>[ constraints ]
>>4 5 1 0.196
> I don't see anything wrong with the topology off hand. You can make
> testing a bit easier by first trying a small box with only CO2 (an odd
> number of molecules!). If that crashes as well on two processors, you
> may send me your input files and I'll have a look.
IIRC, shake blocks (i.e. 'molecules') are generated based on 'connects'.
I don't have the source at hand here, but we should check whether a
'constraint ft=1' also has a 'connect'. If it doesn't, a molecule like
this can be split across processors...
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
| | (Red Hot Chili Peppers) |
More information about the gromacs.org_gmx-users