[gmx-users] rlist

[Faezeh Pousaneh]

Hi,

I have a system of charged hard spheres (user-potential), where the vdW
cut-off should be diameter of my molecule 0.3479. I wonder if I chose rlist
and rcoulomb correctly? (see below please)

integrator                = md
 dt                        = 0.001
 nsteps                    = 30000000
 nstxout                   = 100000           ; save coordinates every 0 ps
 nstvout                   = 100000           ; save velocities every 0 ps
 nstlog                    = 100000           ; update log file every
 nstenergy                 = 100000        ; save energies every
 nstxtcout                 = 100000       ; Output frequency for xtc file
 xtc-precision             = 100000       ; precision for xtc file
 ns_type                   = grid        ; search neighboring grid cells
 nstlist                   = 10           ;  fs
 pbc                       = xyz         ; 3-D PBC
 rlist                          = 0.9         ; short-range neighbor-list
cutoff (in nm)
 rcoulomb                  = 0.9         ; short-range electrostatic cutoff
(in nm)
 rvdw                      = 0.3479      ; short-range van der Waals cutoff
(in nm)
 coulombtype               = PME-user         ; Particle Mesh Ewald for
long-range electrostatics
 pme_order                 = 4           ; cubic interpolation
 fourierspacing            = 0.16        ; grid spacing for FFT
 vdw-type                  = user
 Tcoupl                    = berendsen   ; modified Berendsen thermostat
 tc-grps                   = co2   rest           ; two coupling groups -
more accurate
 tau_t                     =  0.1   0.1 ; time constant, in ps
 ref_t                     =  179.8  179.8 ; reference temperature, one for
each group, in K
 ;tc-grps                  = system
cutoff-scheme              =group
 energygrps                = co2 rest
 Pcoupl                    =  berendsen ;Parrinello-Rahman
 Pcoupltype                = Isotropic
 tau_p                     = 1.0
 compressibility           = 6.2e-5
 ref_p                     = 5500.0
 gen_vel                   = yes
 gen_temp                  = 179.8
 gen_seed                  = 712349
 DispCorr                  =no;  EnerPres    ; account for cut-off vdW
scheme
 constraints               = all-bonds   ; all bonds constrained (fixed
length)
 continuation              = no         ; Restarting after NPT
 constraint-algorithm      =  lincs       ; holonomic constraints
 lincs_iter                = 1           ; accuracy of LINCS
 lincs_order               = 4           ; also related to accuracy
Best regards