GROMACS version:2021.4
GROMACS modification: Yes/No
Here post your question : While building a biphasic system of cyclohexane and water, it’s suggested to change of C radius (in vdwradii.dat file) from 0.17 to 0.35, during the solvation step. Do we need to change the C-radius value to 0.17 agin after the solvation step, for further steps, or should be kept 0.35 throughout all further steps ?
Hi, the vdW radii (C12 or equiv. sigma parameters) are defined in the topology files in later steps, so I think there’s no need to change/reset vdwradii.dat, unless you want to run gmx solvate again. In my experience, using -scale and/or -radius flags was more convenient, and, to be fair, very accurate numbers were never crucial at the solvation step.
I wanted to know, as I was following biphasic tutorial step by step( I placed protein then solvated), so the pressure coupling should be semi-isotropic right?