[gmx-users] Equilibration Error, Skew Factor
Hemant Khoba
up201700003 at g.uporto.pt
Thu Aug 1 18:45:40 CEST 2019
Hello,
I am working on a coarse-grained polymer system having various chain length
(20 & 62), dissolved in water with different counter-ion concentrations.
While equilibrating the systems I am consistently facing an error.
For chain Length 20;
Fatal error:
The X-size of the box (6.716921) times the triclinic skew factor (1.000000)
is
smaller than the number of DD cells (4) times the smallest allowed cell size
(1.680000)
For chain length 62;
Fatal error:
The X-size of the box (11.840870) times the triclinic skew factor (1.000000)
is smaller than the number of DD cells (8) times the smallest allowed cell
size (1.480000)
I have accurately calculated the box size to maintain a particular ion
concentration. 9.8 cubic box for chain length 20 and 18 nm cubic box for
chain length 62.
attached are the .mdp's for temperature and pressure equilibration. Any
suggestions would be highly appreciated.
Thanking you in advance.
Regards,
Hemant Khoba
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08/01/19,
05:42:21 PM
-------------- next part --------------
; minim.mdp - used as input into grompp to generate em.tpr
;
; Run parameters
integrator = steep ; Algorithm (steep = steepest descent minimization)
tinit = 0
dt = 0.002
init-step = 0
comm-mode = Linear
nstcomm = 100
comm-grps = system
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.002 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform
;
; Output control
nstxout = 500 ; save coordinates every 1 ps
nstvout = 500 ; save velocities every 1 ps
nstenergy = 500 ; save energies every 1 ps
nstxtcout = 500 ; co-ordinates to xtc
nstlog = 500 ; update log file every 1.0 ps
nstfout = 500
nstcalcenergy = 100 ; calculate energies
nstcheckpoint = 1000
xtc-precision = 1000
xtc_grps = system
;
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric = 0
ld-seed = -1
;
; Max number of iterations in relax_shells
niter = 20
;
; NEIGHBOR SEARCHING
cutoff-scheme = Verlet
ns-type = grid ; Method to determine neighbor list (simple, grid)
nstlist = 10 ; Frequency to update the neighbor list and long range forces
rlist = 1.0
rvdw = 1.0 ; Short-range Van der Waals cut-off
verlet-buffer-tolerance = 0.005
pbc = xyz ; Periodic Boundary Conditions (yes/no)
periodic_molecules = no
;
; ELECTROSTATICS
coulombtype = PME ; Treatment of long range electrostatic interactions
pme-order = 8
rcoulomb = 1.2 ; Short-range electrostatic cut-off
rcoulomb-switch = 0
epsilon-r = 1 ; 2.5 (with polarizable water)
epsilon-rf = 1
;
; VAN DER WAALS
vdwtype = Cut-off
vdw-modifier = Potential-shift-verlet
;
; CUT-OFF LENGHTS
rvdw-switch = 0
;
; Ewald
DispCorr = EnerPres ;Apply long range dispersion corrections for Energy and Pressure
table-extension = 1
energygrp-table =
fourierspacing = 0.15
fourier-nx = 0
fourier-ny = 0
fourier-nz = 0
ewald-rtol = 1e-05
ewald-rtol-lj = 1e-3
ewald-geometry = 3d
lj-pme-comb-rule = Geometric
epsilon-surface = 0
optimize_fft = yes
;
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = No
tc-grps =
tau-t =
ref-t =
pcoupl = No
pcoupltype = Isotropic
tau-p = 1
ref-p =
refcoord_scaling = No
andersen_seed = 815131
;
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
gen-temp = 300
gen_seed = -1 ;173529
;
; OPTIONS FOR BONDS
constraints = none
constraint-algorithm = LINCS
continuation = no
Shake-SOR = no
shake-tol = 0.0001
lincs-order = 8
lincs-iter = 1
lincs-warnangle = 30
morse = no
-------------- next part --------------
title = Thermorun
define = -DPOSRES ; position restrain the protein
;
; Run parameters
integrator = md-vv ; velocity verlet
nsteps = 25000000 ; 2 * 25000000 = 50 ns
dt = 0.002 ; 2 fs
init_step = 0
energygrps = System
;
; 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
nstxtcout = 500 ; co-ordinates to xtc
nstlog = 500 ; update log file every 1.0 ps
nstfout = 500
nstcalcenergy = 500 ; calculate energies
nstcheckpoint = 1000
xtc-precision = 1000
xtc_grps = System
;
; Neighbor searching
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
rlist = 1.0 ; in nm
verlet-buffer-tolerance = 0.005
;
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme-order = 8 ; 4 is cubic interpolation
rcoulomb-switch = 0
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm); With Verlet rcoulomb!=rvdw is not supported ; For PME rcouloumb>rvdw is possible
epsilon_r = 2.5
;
; Vanderwaals
vdwtype = Cut-off
vdw-modifier = Potential-shift-verlet
rvdw-switch = 0
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
DispCorr = EnerPres ; account for cut-off vdW scheme
;
; Ewald
fourierspacing = 0.15
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
ewald_rtol = 1e-5
ewald-rtol-lj = 1e-3
ewald_geometry = 3d
lj-pme-comb-rule = Geometric
epsilon_surface = 0
optimize_fft = yes
;
; Bond parameters
constraints = none ; all bonds (even heavy atom-H bonds) constrained
constraint_algorithm = LINCS ; holonomic constraints
continuation = no ; first dynamics run
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 8 ; also related to accuracy
lincs_warnangle = 90
shake_tol = 0.0001
morse = no
;
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = System ; two coupling groups - more accurate
nsttcouple = 1 ; frequency for coupling temperature
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
;
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
-------------- next part --------------
title = Barostat
define = -DPOSRES ; position restrain the protein
;
; Run parameters
integrator = md-vv ; verlet celocity
nsteps = 25000000 ; 2 * 25000000 = 50 ns
dt = 0.002 ; 2 fs
init_step = 0
energygrps = System
;
; Output control
nstxout = 500 ; save coordinates every 1 ps
nstvout = 500 ; save velocities every 1 ps
nstenergy = 500 ; save energies every 1 ps
nstxtcout = 500 ; co-ordinates to xtc
nstlog = 500 ; update log file every 1.0 ps
nstfout = 500
nstcalcenergy = 500 ; calculate energies
nstcheckpoint = 1000
xtc-precision = 1000
xtc_grps = System
;
; Neighbor searching
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rlist = 1.0 ; in nm
verlet-buffer-tolerance = 0.005
;
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme-order = 8 ; 4 is cubic interpolation
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rcoulomb-switch = 0
epsilon_r = 2.5
;
; VANDERWAALS
vdwtype = Cut-off
vdw-modifier = Potential-shift-verlet
rvdw-switch = 0
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
DispCorr = EnerPres ; account for cut-off vdW scheme
;
; EWALD
fourierspacing = 0.15 ;grid spacing for FFT (0.15 is reccommended according to manual)
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
ewald_rtol = 1e-5 ;relative strenght of Ewald-shifted direct potential at rcoulomb
ewald-rtol-lj = 1e-3
ewald_geometry = 3d
lj-pme-comb-rule = Geometric
epsilon_surface = 0
optimize_fft = yes
;
; Bond parameters
constraints = none ; all bonds (even heavy atom-H bonds) constrained
continuation = yes ; Restarting after NVT
constraint_algorithm = lINCS ; holonomic constraints
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 8 ; also related to accuracy
lincs_warnangle = 90
shake_tol = 0.0001
morse = no
;
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = System ; two coupling groups - more accurate
nsttcouple = 1 ; frequency for coupling temperature
tau_t = 0.1 ; time constant, in ps. For production with NH, use 2 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 = 12.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 3e-4 ; isothermal compressibility of water, bar^-1
refcoord_scaling = com
;
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
;
;
; Velocity generation
gen-vel = no ; Velocity generation is off
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