Hi Users,
I have a polymer ensemble with flexible side chains. I would like to thermally treat the system so the side chains can flop around but I don’t want the backbone to loose it’s original “shape”. I was thinking I could make the dihedral force constant high for the backbone but that just sounds like a dumb idea. My next thought is to use “fix rigid”. Does that sound like the LAMMPS way?
Thanks
How about fix spring/self?
Axel
Thanks Axel for the suggestion but I’d still like the polymer to move as a whole. Basically I want the backbone to keep it’s starting conformation, the side chains to flop around and the entire chain able to move around the box. I’m doing this to equilibrate the side chains while retaining backbone configuration.
Thanks Axel for the suggestion but I'd still like the polymer to move as a
whole. Basically I want the backbone to keep it's starting conformation, the
side chains to flop around and the entire chain able to move around the box.
I'm doing this to equilibrate the side chains while retaining backbone
configuration.
well, your original idea of using stiff dihedrals is one option. using
fix rigid might work as well, if you would assign different molecule
ids to the backbone vs. the side chains, yet another option would be
to use the colvars module to apply a conformation restraint to the
backbone atoms. colvars has some rather sophisticated collective
variables that allow retaining conformation without making the
structure too rigid (which might interfere with the relaxation that
you are after).
in general, while for production calculations one has to be very
careful which system manipulations are applied, during equilibration
all bets are off and anything that gets you quickly to where you need
to get is allowed.
axel.