Dear Gromacs users, I am simulating a system that contains a drug nanoparticle in amorphous state, surrounded by water and the water is also surrounded by acetone (imagine 2 concentric spheres for the first two inside one big box for the acetone).
I used to build the system using gromacs editconf and more precisely building one box at a time and running em, nvt and npt equilibration for each one of the extra box-layers I was adding. However this was a very tedious procedure so I have started recently building the system using Packmol. Once I get the pdb from packmol I edit it to add the box dimensions with editconf and then go through an em, nvt, npt (usually 100ps) for the whole system. I have already run 4-5 simulations of 50ns and 100ns and they were running fine (they are running on parallel in a cluster). However in my last one I got the following error: Fatal error: 1 particles communicated to PME node 20 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. I know this means that the system is not well equilibrated but after the nvt and npt the T and P are converged. I have reduced the time step to 1fs but I am also worried that the equilibration is not the correct one. It is also worth saying that I had similar errors even with my previous building procedure using gromacs. Any suggestions/experiences with using Packmol? I am also attaching my mdp options below just in case. Thank you very much for your time in advance, Ioanna Styliari EM: integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 10.0 ; Stop minimization when the maximum force < 10.0 kJ/mol/nm emstep = 0.001 ; Energy step size nsteps = 500000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbours of each atom and how to calculate the interactions Nstlist = 1 ; Frequency to update the neighbour list and long range forces ns_type = grid ; Method to determine neighbour list (simple, grid) rlist = 1.0 ; Cut-off for making neighbour list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; Short-range electrostatic cut-off vdw-type = Cut-off rvdw = 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions NVT title = pol1-box NVT ; Run parameters integrator = md ; nsteps = 100000 ; 100 ps dt = 0.001 ; 1 fs ; Bond parameters continuation = no ; first dynamics run ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = system ; tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed constraints = none NPT title = pol1-box NPT ; Run parameters integrator = md nsteps = 100000 dt = 0.001 ; Bond parameters continuation = yes ; Restarting after NVT ; Neighborsearching ns_type = grid ; search neighbouring grid cells nstlist = 5 ; fs rlist = 1.0 ; short-range neighbourlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = system ; tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = berendsen ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off and then MD: title = pol1-box first 2 ns MD ; Run parameters integrator = md ; nsteps = 2000000 ; dt = 0.001 ; fs ; Bond parameters continuation = yes ; Restarting after NPT ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = system ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off This message and any attachment are intended solely for the addressee and may contain confidential information. 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