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.
Cutoffs can certainly have an effect on the configuration of the system. The
cutoffs define the short-range interactions, and thus the way the particles
associate with one another. As for the second .mdp file, I really don't see any
feasible reason to use a 0.3-nm cutoff for rcoulomb and rlist; this is
incredibly short and you are likely truncating prematurely. What force field
are you using? Surely you should be using parameters related to what is
specified in the original derivation of the parameter set.
-Justin
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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