[gmx-users] grompp segmentation fault when trying to position restrain water along bilayer normal
x.periole at rug.nl
Tue Mar 17 17:09:59 CET 2009
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 :
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.
do not retrain the atoms you think.
then I would only retrain the oxygen of the water molecules, hydrogens
need to move.
On Mar 17, 2009, at 4:56 PM, maria goranovic wrote:
> 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
> 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
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