How to apply position restrain on one molecule in umbrella sampling?

User discussions
1

GROMACS version: 2021.4
GROMACS modification: Yes/No
Hi all,
In umbrella sampling, We try to extract the potential of mean force (PMF) by adding a center-of-mass (COM) pulling (in pull code) between two identical types of molecules. I want to restrain the position of one molecule, whereas the second molecule will be free to move.
Can you please help how I can do that?

Thank you for your responses in advance.

Kind regards,
Bappaditya

2

Since restraints are applied on the topology level, you need to have two copies of the same [moleculetype] and assign them different names. Then you can apply restraints within one of those [moleculetype] entries.

3

Thank you for your valuable reply.