[gmx-users] position restraints

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 24 10:48:01 CEST 2008

gadies at fh.huji.ac.il wrote:

Please generate replies to the mailing list sensibly. It's very hard to 
work out who you are quoting where in this email. It'd be easy just to 
ignore it, and that's the last thing you should want.

> Hello,
> I'm trying to run a simulation with one lipid molecule in a fixed
> simulation box without pbc.
> I set position restraints on one of the atoms and I seem to keep on
> getting the following error:

Why do you want MD of a single lipid and a position restraint on one 
atom? If you just want to see a lipid wiggle around, then don't create 
more numerical complexity.

> The lipid is DPPC.The .itp file I got from a coworker that used it 
> before for membrane MD simulations.
> To minimize the system I used steepest descent with the following 
> parameters:

Well if your grompp and mdrun completed successfully and without 
warnings then you've probably got an OK topology and structure.

The combination of all bond constraints, a single lipid in vacuo, 
temperature coupling and a single position restraint sounds like a 
recipe for a numerical disaster, i.e. blowing up. Try with fewer of 
those things applied, or get a more physically-reasonable system, like a 
whole membrane.


More information about the gromacs.org_gmx-users mailing list