[gmx-users] Flat bottom position restraints
sabine.reisser at kit.edu
Fri Feb 13 14:11:41 CET 2015
Here's the pdf.
Am 13.02.2015 14:03, schrieb Sabine Reisser:
> Ok, I figured it out. With inverse FB pos res, the atoms are pushed away
> from there initial positions. Compare attached pdf, which shows the z
> coordinate of the first atom of 3 peptides, with and without the
> position restraints defined below.
> Since you cannot define the direction to which the atoms/peptides are
> pushed, this doesn't help in my case.
> Am 13.02.2015 12:14, schrieb Sabine Reisser:
>> 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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