Hi, I am new to molecular dynamics and gromacs. I am working on a project with the goal to study the effect of mutation on the overall structure and stability of a protein. There is no experimental model available, and I am currently working with an AlphaFold model.While performing NVT equilibration I am getting the following error (details are below). Fatal error:
2608 particles communicated to PME rank 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated.
Here are the details of my NVT.mdp file :
; NVT Equilibration
title = NVT equilibration
define = -DPOSRES ; position restraints
integrator = md
dt = 0.002
nsteps = 50000 ; 100 ps
nstxout = 1000
nstvout = 1000
nstenergy = 1000
nstlog = 1000
continuation = no
constraint_algorithm = lincs
constraints = h-bonds
cutoff-scheme = Verlet
ns_type = grid
nstlist = 20
rcoulomb = 1.2
rvdw = 1.2
vdwtype = Switch
rvdw-switch = 1.0
coulombtype = PME
pbc = xyz
tcoupl = V-rescale
tc-grps = Protein Water_and_ions
tau_t = 0.1 0.1
ref_t = 310 310
pcoupl = no
gen_vel = yes
gen_temp = 310
gen_seed = -1
Also, I would like to mention that when I am performing the energy minimization step the minimizer ran for 18,077 steps. The run stopped because, according to the GROMACS message: “…the algorithm tried to make a new step whose size was too small, or there was no change in the energy since the last step.” My em.mdp file I set emtol = 10.0 but the minimization stopped with a Maximum force = 3.6917218e+02 (which is 369.17 kJ/mol/nm) on atom 721. However, I continued with the next steps. I do not know if the error at the NVT equilibration has to do anything with this previous step.