GROMACS version: 2019.2/4
Dear Gromacs Users,
There is a way to implement a positional restraint on the center of mass of a specific group?
I only found restraint applied to physical atoms in the manual.
Thank you for your kind attention.
No, but you might achieve a similar effect using a spherical flat-bottom restraint on the selected atoms.
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So I assume distance restraints on COM of groups is out of the question. (2020.1) Are there any pitfalls I might fall into if I try to set restraints between all inter group pairs of atoms, that are already known?
The pull code allows for restraints to be set based on COM distances between specified groups. Distance restraints (which are specified in the topology, not the .mdp file) can be set between any pairs of atoms.
So since I already have the groups defined as pull groups I can just apply a pull force with a zero rate to maintain the distance?
Yes, that’s you’d do it.
I tried the pull code but when my ligand crossed the periodic boundary with the binding site remaining on the other side, the simulation failed.
I was told that I could use a distance restraint but that appears to only work within the same molecule type. I tried to create a distance restraint between a ligand carbon and an amino acid sidechain atom but got the grompp error about the restraint being placed in the wrong molecule section.
I believe the Plumed “Walls” option will work but was hoping to find a way by only using gromacs options.
If I understand correctly, the spherical restraint would not allow the ligand to move freely within the binding site if the protein rotated away from the restrained region.