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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