Lum Nforbi wrote:
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.
If your rdf goes to zero you have a gas. Your box has probably expanded
a lot. Please check the density.
.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
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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