[gmx-users] the segmentation fault for MD with constraints=none!

David van der Spoel spoel at xray.bmc.uu.se
Tue Nov 21 15:46:57 CET 2006

Rongliang Wu wrote:
> dear all,
> thanks for your great suggestions and i have met with new problems in
> simulation of bulk systems or crystal cells when no constraints are
> utilized, the systems either explode or met with "segmentation fault"!
> and i am sure my systems are well minimized.
> and again when constraints= all-angles, the system often collapse.
> i have always being using the all-bonds constraints, but the bond length
> distribution can no be thus derived.
> the constraint parameters in mdp files are defaults!
> best regards!
Please state clearly
+ objective
+ what you have tried
+ if there were problems

If I read you correctly you want to study bond length distributions, in
which case you need to turn off constraints and reduce the timestep to
0.2 and 0.5 fs.

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

More information about the gromacs.org_gmx-users mailing list