[gmx-users] Re: Segmentation Error

Pim Schravendijk schraven at mpip-mainz.mpg.de
Wed Mar 17 13:04:01 CET 2004

Dear Farshid,

You might want to read this thread:


For a completely hard wall, this might be the solution of your problem:


For "softer" walls you could replace this function reversing the
velocities by a repulsive potential of some sort.

Greetings, Pim

Pim Schravendijk - PhD Student
Max Planck Institute for Polymer Research

> -----Forwarded Message-----
> >From: Farshid Mostowfi <farshid at ualberta.ca>
> >To: David van der Spoel <spoel at xray.bmc.uu.se>
> >Subject: Segmentation Error
> >Date: Tue, 16 Mar 2004 11:43:21 -0700
> >
> >Dear David;
> >
> >I have a problem with Gromacs. I sent my question to the gromacs user mail 
> >list twice but nobody answered. I was wondering whether you could help me out.
> >I'm simulating a small box of water with a few NA+ and CL- ions in it. For
> >long range correction everything worked perfectly with PME, but when I used
> >Ewald, I got "Segmentation Error" from mdrun (while energy minimizing and 
> >simulating). Could you please help me out.
> Don't know, might be a bug.
> >I also have another question, in the next step I want to cancel periodic 
> >boundary condition from two of the parallel walls. Actualy I want to make a 
> >hard wall. Is it possible to do that? If yes could you please let me know how?
> It's not implemented, but quite easy to do. Either you can have a set of fixed particles
> or hardcode it in the update routines.
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assist. 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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