User-defined potential for position restraints

User discussions
1

GROMACS version: 2019.6
GROMACS modification: Yes/No
Hi, I’m new to GROMACS and have recently been applying cylindrical shaped position restraint on a group of atoms with the GROMACS built-in flat-bottomed potential. However, I want to switch to an arbitrary potential which I don’t think GROMACS have it. I’m wondering if there has way to implement a cylindrical shaped position restrain on a group of atoms with an user-defined potential in GROMACS. Any help toward this is greatly appreciated.

2

Hi,

GROMACS has three flat-bottomed potentials that can be used position restrain: sphere, cylinder, layer
(see http://manual.gromacs.org/documentation/current/reference-manual/functions/restraints.html?highlight=position%20restrain).
Does any of those work for you?
I do not know if there is any option to change restrain potential formula from the input files.

Kind regards
Alessandra

3

Hi Alessandra,
Thanks for your reply! I’m particularly interested if one can change the restrain potential formula, but what you said is also helpful for me!
SIncerely

4

Hi,
you could always try to modify the potential in the source code.
Kind regards
Alessandra

5

Hi Alessandra,
Thanks! I’ll try to do something you said.
Sincerely