I do not believe it is because of packmol or because of equilibration. What about trying a different number of cores per job? Sometimes, certain number of cores do not want to work correctly for certain systems.
Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Wed, Oct 29, 2014 at 7:07 PM, Ioanna Styliari <pax...@nottingham.ac.uk> wrote: > 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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