[gmx-users] grompp segmentation fault when trying to position restrain water along bilayer normal

[XAvier Periole]

You've probably conflicts of restrains and forces in your system.

Note that our definition of the position restraints if applicable to
all solvent molecules should be :

[position_restraints]
1 1 0 0 1000
2 1 0 0 1000
3 1 0 0 1000

if not it will look at the atom of the solvent number 34083 ... etc.  
You basically
do not retrain the atoms you think.

then I would only retrain the oxygen of the water molecules, hydrogens  
might
need to move.

On Mar 17, 2009, at 4:56 PM, maria goranovic wrote:

> Hello
>
> I am trying to restrain water along the bilayer normal. For this;
>
> 1.  I made a posre_solvent.itp using genpr. It look like this:
>
> ; position restraints for Solvent
>
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
> 34083    1          0          0       1000
> 34084    1          0          0       1000
> 34085    1          0          0       1000
> ... (there are ~ 60,000 water molecules)
>
> 2. I include this file in my topology file using:
>
> #ifdef POSRES_SOLVENT
> #include posre_solvent.itp
> #endif
>
> 3. And finally, the mdp file looks like:
> ..
> define              =   -DFLEX_SPC -DPOSRES_SOLVENT
> ..
>
> Why do I get a segmentation fault on running grompp?
>
> Thank u for helping
>
> -- 
> Maria G.
> Technical University of Denmark
> Copenhagen
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php