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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
