GROMACS version: 2021
GROMACS modification: No
Hi, recently I’m reading a paper which use gromacs to do simulation. The author said that:
I think decreasing the time step is easy to do in Gromacs, but how about turning off the bond constraint? Do I need to modify the topology file? Or should I set the constraints=none in mdp file?
Hi,
The use of bond constraints is linked to the force field one use. If the force field required for time-step 0.002 ps constraints on the hydrogen atoms. One can not remove the constraints on bond involving hydrogen, since that can make the simulation inaccurate and sometimes even unstable.
Best regards
Alessandra
Hi, I’m using GAFF2 for small ligand, Can I do that?
