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
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