[gmx-users] Packmol starting .pdb and proper equilibration

[Ioanna Styliari]

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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