[gmx-users] Packmol starting .pdb and proper equilibration
Ioanna Styliari
paxids at nottingham.ac.uk
Wed Oct 29 19:08:22 CET 2014
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
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