[gmx-users] Cut-offs in gromacs
Justin A. Lemkul
jalemkul at vt.edu
Tue Feb 23 04:11:06 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.
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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