[gmx-users] Domain Decomposition

[Shraddha Parate]

Dear Gromacs Users,

I was able to achieve a spherical water droplet without periodic boundary
conditions (PBC) by changing few parameters in the .mdp files as below:

*minim.mdp:*
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0  ; Stop minimization when the maximum force < 1000.0
kJ/mol/nm
emstep          = 0.01          ; Energy step size
nsteps = 50000   ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 0 ; Frequency to update the neighbor list and long range forces
cutoff-scheme   = Group
ns_type = simple ; Method to determine neighbor list (simple, grid)
rlist = 0.0 ; Cut-off for making neighbor list (short range forces)
coulombtype = Cut-off ; Treatment of long range electrostatic interactions
rcoulomb = 0.0 ; Short-range electrostatic cut-off
rvdw = 0.0 ; Short-range Van der Waals cut-off
pbc = no ; Periodic Boundary Conditions (yes/no)


*nvt.mdp:*
title = OPLS Lysozyme NVT equilibration
define = -DPOSRES ; position restrain the protein

; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000         ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs

; Output control
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps

; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
comm_mode        = ANGULAR
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy

; Neighborsearching
ns_type = simple ; search neighboring grid cells
nstlist = 0 ; 10 fs
rlist = 0.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 0.0 ; short-range electrostatic cutoff (in nm)
rvdw = 0.0 ; short-range van der Waals cutoff (in nm)
verlet-buffer-drift = -1

; Electrostatics
cutoff-scheme   = Group
coulombtype = Cut-off ; 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 = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K

; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT

; Periodic boundary conditions
pbc = no ; 3-D PBC

; Dispersion correction
DispCorr = No ; 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




*npt.mdp:*
title = OPLS Lysozyme NPT equilibration
define = -DPOSRES ; position restrain the protein

; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100 ps
dt     = 0.002 ; 2 fs

; Output control
nstxout = 500 ; save coordinates every 1.0 ps
nstvout = 500 ; save velocities every 1.0 ps
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps

; Bond parameters
continuation         = no ; Restarting after NVT
constraint_algorithm    = lincs     ; holonomic constraints
constraints             = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
comm_mode        = ANGULAR
lincs_iter             = 1     ; accuracy of LINCS
lincs_order             = 4     ; also related to accuracy

; Neighborsearching
cutoff-scheme   = Group
ns_type     = simple ; search neighboring grid cells
nstlist     = 0     ; 20 fs, largely irrelevant with Verlet scheme
rlist = 0.0 ; short-range neighborlist cutoff (in nm)
rcoulomb     = 0.0 ; short-range electrostatic cutoff (in nm)
rvdw     = 0.0 ; short-range van der Waals cutoff (in nm)
verlet-buffer-drift = -1

; Electrostatics
coulombtype     = Cut-off ; 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 = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1   0.1         ; time constant, in ps
ref_t = 300   300         ; reference temperature, one for each group, in K

; Pressure coupling is on
pcoupl         = No     ; 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 = no ; 3-D PBC

; Dispersion correction
DispCorr = No ; account for cut-off vdW scheme

; Velocity generation
gen_vel = no ; Velocity generation is off





*md.mdp:*
title = OPLS Lysozyme MD simulation

; Run parameters
integrator = md ; leap-frog integrator
nsteps = 500000 ; 2 * 500000 = 1000 ps (1 ns)
dt     = 0.002 ; 2 fs

; Output control
nstxout         = 5000 ; save coordinates every 10.0 ps
nstvout         = 5000 ; save velocities every 10.0 ps
nstenergy         = 5000 ; save energies every 10.0 ps
nstlog         = 5000 ; update log file every 10.0 ps
nstxout-compressed  = 5000      ; save compressed coordinates every 10.0 ps
                                ; nstxout-compressed replaces nstxtcout
compressed-x-grps   = System    ; replaces xtc-grps

; Bond parameters
continuation         = yes ; Restarting after NPT
constraint_algorithm    = lincs     ; holonomic constraints
constraints             = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
comm_mode        = ANGULAR
lincs_iter             = 1     ; accuracy of LINCS
lincs_order             = 4     ; also related to accuracy

; Neighborsearching
cutoff-scheme   = Group
ns_type     = simple ; search neighboring grid cells
nstlist     = 0     ; 20 fs, largely irrelevant with Verlet scheme
rlist = 0.0 ; short-range neighborlist cutoff (in nm)
rcoulomb     = 0.0 ; short-range electrostatic cutoff (in nm)
rvdw     = 0.0 ; short-range van der Waals cutoff (in nm)


; Electrostatics
coulombtype     = Cut-off ; 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 = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1   0.1         ; time constant, in ps
ref_t = 300   300         ; reference temperature, one for each group, in K

; Pressure coupling is on
pcoupl         = no     ; 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 = no ; 3-D PBC

; Dispersion correction
DispCorr = No ; account for cut-off vdW scheme

; Velocity generation
gen_vel = no ; Velocity generation is off



However, I am facing the following error:

*Fatal error:*
*Domain decomposition does not support simple neighbor searching, use grid
searching or run with one MPI rank.*

I tried adding the '-nt 1' in the command for mdrun but it consumes 2 weeks
for a 1 ns simulation since it utilizes only 1 CPU.

Is the error occurring because of changes in .mdp file parameters? Is there
any other way to make some changes in the mdrun command to make the
simulation faster?

Thank you in advance.

Best regards,
Shraddha Parate