[gmx-users] Cut-offs in gromacs

Lum Nforbi lumngwegia at gmail.com
Tue Feb 23 03:53:29 CET 2010


Dear all,

        I did two md simulations of 200 particles each of a lennard-jones
fluid. One of them gave me the correct pair distribution function for a
lennard-jones fluid (converging to 1) and one did not (converging to zero).
I have attached the .mdp files for both systems below. The barostats are
different but I don't think this is the cause. I think that one worked
because of the cut-off specifications (rlist, rvdw and rcoulomb), but I am
not sure of the explanation of how the cut-off values can influence the
shape of a pair distribution function. The fourier spacing in both parameter
files are also different.
        Please, if someone knows how these cut-off values and maybe fourier
spacing could influence the shape of a pair distribution function, let me
know the explanation.

.mdp file which gave the plot which converges to zero:

title                    = NPT simulation of a LJ FLUID
cpp                      = /lib/cpp
include                  = -I../top
define                   =
integrator               = md         ; a leap-frog algorithm for
integrating Newton's equations of motion
dt                       = 0.002      ; time-step in ps
nsteps                   = 500000     ; total number of steps; total time (1
ns)
nstcomm                  = 1          ; frequency for com removal
nstxout                  = 500        ; freq. x_out
nstvout                  = 500        ; freq. v_out
nstfout                  = 0          ; freq. f_out
nstlog                   = 50         ; energies to log file
nstenergy                = 50         ; energies to energy file
nstlist                  = 10         ; frequency to update neighbour list
ns_type                  = grid       ; neighbour searching type
rlist                    = 1.0        ; cut-off distance for the short range
neighbour list
pbc                      = xyz        ; Periodic boundary conditions:xyz,
use periodic boundary conditions in all directions
periodic_molecules       = no         ; molecules are finite, fast molecular
pbc can be used
coulombtype              = PME        ; particle-mesh-ewald electrostatics
rcoulomb                 = 1.0        ; distance for the coulomb cut-off
vdw-type                 = Cut-off    ; van der Waals interactions
rvdw                     = 1.0        ; distance for the LJ or Buckingham
cut-off
fourierspacing           = 0.12       ; max. grid spacing for the FFT grid
for PME
fourier_nx               = 0          ; highest magnitude in reciprocal
space when using Ewald
fourier_ny               = 0          ; highest magnitude in reciprocal
space when using Ewald
fourier_nz               = 0          ; highest magnitude in reciprocal
space when using Ewald
pme_order                = 4          ; cubic interpolation order for PME
ewald_rtol               = 1e-5       ; relative strength of the
Ewald-shifted direct potential
optimize_fft             = yes        ; calculate optimal FFT plan for the
grid at start up.
DispCorr                 = no         ;
Tcoupl                   = v-rescale  ; temp. coupling with vel. rescaling
with a stochastic term.
tau_t                    = 0.1        ; time constant for coupling
tc-grps                  = OXY        ; groups to couple separately to temp.
bath
ref_t                    = 80         ; ref. temp. for coupling
Pcoupl                   = berendsen  ; exponential relaxation pressure
coupling (box is scaled every timestep)
Pcoupltype               = isotropic  ; box expands or contracts evenly in
all directions (xyz) to maintain proper pressure
tau_p                    = 0.5        ; time constant for coupling (ps)
compressibility          = 4.5e-5     ; compressibility of solvent used in
simulation
ref_p                    = 1.0        ; ref. pressure for coupling (bar)
gen_vel                  = yes        ; generate velocities according to a
Maxwell distr. at gen_temp
gen_temp                 = 80         ; temperature for Maxwell distribution
gen_seed                 = 173529     ; used to initialize random generator
for random velocities

.mdp file which gave the plot which converges to 1:

title                    = NPT simulation of a LJ FLUID
cpp                      = /lib/cpp
include                  = -I../top
define                   =
integrator               = md           ; a leap-frog algorithm for
integrating Newton's equations of motion
dt                       = 0.002        ; time-step in ps
nsteps                   = 500000       ; total number of steps; total time
(1 ns)
nstcomm                  = 1            ; frequency for com removal
nstxout                  = 1000         ; freq. x_out
nstvout                  = 1000         ; freq. v_out
nstfout                  = 0            ; freq. f_out
nstlog                   = 500          ; energies to log file
nstenergy                = 500          ; energies to energy file
nstlist                  = 10           ; frequency to update neighbour list
ns_type                  = grid         ; neighbour searching type
rlist                    = 0.3          ; cut-off distance for the short
range neighbour list
pbc                      = xyz          ; Periodic boundary conditions:xyz,
use p b c in all directions
periodic_molecules       = no           ; molecules are finite, fast
molecular pbc can be used
coulombtype              = PME          ; particle-mesh-ewald electrostatics
rcoulomb                 = 0.3          ; distance for the coulomb cut-off
vdw-type                 = Cut-off      ; van der Waals interactions
rvdw                     = 0.7          ; distance for the LJ or Buckingham
cut-off
fourierspacing           = 0.135        ; max. grid spacing for the FFT grid
for PME
fourier_nx               = 0            ; highest magnitude in reciprocal
space when using Ewald
fourier_ny               = 0            ; highest magnitude in reciprocal
space when using Ewald
fourier_nz               = 0            ; highest magnitude in reciprocal
space when using Ewald
pme_order                = 4            ; cubic interpolation order for PME
ewald_rtol               = 1e-5         ; relative strength of the
Ewald-shifted direct potential
optimize_fft             = yes          ; calculate optimal FFT plan for the
grid at start up.
DispCorr                 = no
Tcoupl                   = nose-hoover; temp. coupling with vel. rescaling
with a stochastic term.
tau_t                    = 0.5        ; time constant for coupling
tc-grps                  = OXY        ; groups to couple separately to temp.
bath
ref_t                    = 80         ; ref. temp. for coupling
Pcoupl                   = parrinello-rahman  ; exponential relaxation
pressure coupling (box is scaled every timestep)
Pcoupltype               = isotropic  ; box expands or contracts evenly in
all directions (xyz) to maintain proper pressure
tau_p                    = 5.0        ; time constant for coupling (ps)
compressibility          = 4.5e-5     ; compressibility of solvent used in
simulation
ref_p                    = 1.0        ; ref. pressure for coupling (bar)
gen_vel                  = yes        ; generate velocities according to a
Maxwell distr. at gen_temp
gen_temp                 = 80         ; temperature for Maxwell distribution
gen_seed                 = 173529     ; used to initialize random generator
for random velocities

I appreciate your reply.

Lum
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