[gmx-users] rlist

[Justin Lemkul]

On 1/14/18 6:01 AM, Faezeh Pousaneh wrote:
> 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)

I'm not sure if anyone can tell you that. You're using custom 
potentials, so setting cutoffs is part of the parametrization of that 
potential itself.

-Justin

> 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

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================