GROMACS version: 2023.5
GROMACS modification: No
Hi! I’ve been simulating different large protein-membrane systems (> 500k atoms) for a while now to investigate the oligomerisation and membrane interaction of my protein of study. I’ve always prepared the systems with CharmmGUI, but I just noticed that my most recent simulations run with different thermo/barostats to the previous simulations. They switched from Nose-Hoover/Parrinello-Rahman to v-rescale/c-rescale. The rest of the parameters in the mdp file are the same. Here is my latest mdp version:
integrator = md dt = 0.002 nsteps = 500000 nstxout-compressed = 50000 nstxout = 0 nstvout = 0 nstfout = 0 nstcalcenergy = 100 nstenergy = 1000 nstlog = 1000 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 vdwtype = Cut-off vdw-modifier = Force-switch rvdw_switch = 1.0 rvdw = 1.2 coulombtype = PME rcoulomb = 1.2 ; tcoupl = v-rescale tc_grps = SOLU MEMB SOLV tau_t = 1.0 1.0 1.0 ref_t = 303.15 303.15 303.15 ; pcoupl = C-rescale pcoupltype = semiisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; constraints = h-bonds constraint_algorithm = LINCS continuation = yes ; nstcomm = 100 comm_mode = linear comm_grps = SOLU_MEMB SOLV
While I’ve seen on the forum that v-rescale and c-rescale are highly recommended now, I worry that my simulations may not be comparable between them. For instance, if we publish a paper including results from two or more protein-membrane systems (such as the wild-type protein and a mutated version, or different order oligomers, or membrane placements) that have been simulated with different thermo/barostats.
Should I worry about this or is this not a fatal mistake?
Thank you in advance.