[gmx-users] Flat bottom position restraints

Sabine Reisser sabine.reisser at kit.edu
Fri Feb 13 12:14:53 CET 2015


I want to use inverse FB pos res to construct a layer in the xy plane 
where my peptides are not allowed to go, to facilitate binding to the 
upper leaflet of my membrane instead of to the lower leaflet of the 
neighboring periodic image.
In the manual it says I need three parameters
r (nm)
k (force constant).

g would be 5 because I have a layer with a normal parallel to the 
z-axis. k is also clear. r would be the thickness of the layer.
However, when I invert the restraints I understand I would have to give 
the reference position manually (in the manual: "it is possible to 
invert the restrained region with the unrestrained region, leading to a 
potential that acts to keep the particle outside of the volume defined 
by R_i , g, and r_fb").
How do I define the reference position R_i?

[ position_restraints ]
1       2       5       -1      1000

doesn't give an error in grompp but I don't see how mdrun can know where 
to put the layer. Additional parameters are not allowed.

I'd be thankful for a hint on this.


Dipl. Phys. Sabine Reißer
Karlsruhe Institute of Technology (KIT)
Institute of Physical Chemistry

Phone +49 (0) 721 / 608-45070

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