On 10/29/14 2:07 PM, Ioanna Styliari 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.
What is your concern regarding the time step? This is a common strategy for temperamental systems.
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
So in reality there is no difference between NPT and the production run, e.g. no restraints or anything. At what point dos the crash occur? What force field are you using?
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
