Applying flat bottom potential on substrate

[l_aditi]

GROMACS version: 18.8
GROMACS modification: NO

I want to apply flat bottom restraint on my substrate while pulling it in the z direction, such that it will able to move freely in a specific area only.

Content of file I have created:
; Position restraint for substrate
[ position_restraints ]
; i funct g r k
8 2 2 0.7 10000

secondly while doing the final umbrella sampling I used this file:
; Position restraint for substrate
[ position_restraints ]
; i funct g r k
8 2 2 1.0 10000

I wanted to know whether I am mentioning the function and g value correctly or not?
what should be the value of funct and g?

[alevilla]

Hi,
It depends what you want to do. In the following links you find the explanation of function values and of the g (geometry) values

• a value of funct = 2 in the directive [position_restrains] correspond to flat bottom restraints see here for
  https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html
• a values of g = 2 In GROMACS 2022, g=2 setting is mapped g=8 see more here https://manual.gromacs.org/current/reference-manual/functions/restraints.html?highlight=restrain.
  I guess you are using an older GROMACS version (series 2018?), in that case good to cross check with the manual of the corresponding version.

I hope it helps
Alessandra

[l_aditi]

Hello Alessandra,
Thanks for clarifying my doubt.
Actually, what I am trying to do is pull a substrate through a membrane transporter. For this, I am placing the substrate above the protein (in the solvent) and pulling it using a constant force and velocity. Instead of moving through the transporter pore, it is moving just adjacent to the protein’s surface. I tried to increase the pulling force and velocity, but nothing seems to work.
Can you please suggest to me any approach to proceed with?