[gmx-users] Cut-offs in gromacs
David van der Spoel
spoel at xray.bmc.uu.se
Tue Feb 23 09:00:35 CET 2010
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.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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