Does anyone have experience with molecular dynamics simulations in GROMACS with geometry constraints? I know that GROMACS implements LINCS, SHAKE, and SETTLE, in order to constrain chemical bond lengths, angles, etc., and each of these has different capabilities/advantages. That being said, I rarely run constrained simulations.
I am trying to constrain all bond lengths and angles, meanwhile using my own table files (custom force field), and hopefully run on more than 1 CPU.
I run into trouble because the use of custom table files forces me to alter the “charge group” of atoms in molecules, which causes SHAKE to fail on >1 CPU. But LINCS can not constrain angles. My current workaround has been to make all bond angles very stiff by using arbitrarily large angle force constants. This allows the “rigid” simulation to run on multiple CPUs using LINCS, but I won’t generate proper energetics any more.