[gmx-users] Cut-offs in gromacs

[David van der Spoel]

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