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?
Hey,
I know this is long ago but i was wondering what you eventually did and what was your experience. (I am also uncertain on what i should do)
From my understanding, TI was used in the methodology of GAFF2. This was to compare solvation free energy (with GAFF2 VDW+partial charges) to experimental values. With the use of TI, SHAKE was disabled and a smaller time step was used to ensure accurate integration.
Now in order to conduct a normal MD, not TI, i believe we should turn off bond constraint and just use a time step of 1fs like they did but its possible that a smaller time step might even be needed. (i am sort of thinking that lambda = 0 is the same as our system). This would be opposite to normal MD protocols that i know of that uses 2fs with constraint algorithms on hydrogens only.
I just learnt about TI so i might have some errors in my understanding so please feel free to correct me if im wrong
Kind regards,
hehe
