[gmx-users] segmentation fault

David spoel at xray.bmc.uu.se
Sun Aug 15 11:45:25 CEST 2004

On Sat, 2004-08-14 at 22:42, Dinesh Pinisetty wrote:
> Hello everyone,
>         when I was trying to do energy minimization of
> DPPC membrane with water I am getting error as
>   I have added water using genbox command,box is
> cubic.
>   Could anybody tell me what might be the reason for
> this error...................

Could be due to large forces. In fact, almost all SEGV in mdrun are due
to large forces, i.e. non-physical coordinates. This fits well with the
way you built the starting structure.

If you insist on building your own, you might want to start with running
without water, equilibrate and add water after that.

> Thank you.
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
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://xray.bmc.uu.se/~spoel

More information about the gromacs.org_gmx-users mailing list