# NVT Equilibration **URL:** \ **Category:** User discussions\ **Created:** [May 23, 2025, 10:26pm UTC](https://gromacs.bioexcel.eu/t/nvt-equilibration/12146 "2025-05-23T22:26:43Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![Boise](https://avatars.discourse-cdn.com/v4/letter/b/c67d28/32.png) [@Boise](https://gromacs.bioexcel.eu/u/Boise)\ **Post date:** [May 23, 2025, 10:26pm UTC](https://gromacs.bioexcel.eu/t/nvt-equilibration/12146/1 "2025-05-23T22:26:43Z")
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.