GROMACS version: 2020.4
GROMACS modification: No
Hi all,
I’m wondering if there’s a simple way of ‘switching off’ interactions one at a time? I have a polymer in water and I’d like to get some qualitative idea of what’s having the biggest impact on conformation. In particular, I’d like to switch off electrostatics, the dispersion term in the LJ potential (retaining the r^-12 term), and torsional terms. In my head, I imagine effectively having a bunch of hard-spheres on springs (including water), then hard spheres on springs plus electrostatics, then plus torsional energies etc… Ideally the computation of the terms to be switched off could be avoided altogether to get some speed up.
Electrostatics: I’ve found a thread from 2009 where it was suggested to set epsilon_r to zero in the .mdp file. This seems more preferable than setting setting all charges to zero in the topology, as I’d like the water electrostatics to be switched off too (although I guess I could modify the water topology too?).
LJ: This one’s a bit trickier, as I’d like to retain the hard-sphere r^-12 repulsion but switch off the r^-6 attractive term. I suppose I’d need to make a user defined interaction for just the r^-12 term, turn all LJ off, then just use the user defined r^-12 term? If this seems to be the best way to go, please just let me know and if you’re feeling nice, direct me to some resources explaining how.
Torsional terms: I’ve already had success with simply setting the torsional terms in the topology to zero, but perhaps there’s a simpler way that could avoid some unnecessary computations?
Sorry if these are basic questions, I’m happy to simply follow a link if they’ve been answered elsewhere.