[gmx-users] Default cut-off scheme.
mark.j.abraham at gmail.com
Sun Jul 26 00:45:08 CEST 2015
On Sun, Jul 26, 2015 at 12:32 AM Tamisra Pal <tamisra1985 at gmail.com> wrote:
> Hi ,
> The cutoff-scheme by default is Verlet , unless you specify it as group.
> Yes , in this case , the ns_type is grid
... assuming this is version 5. But Dawid will get an accurate answer much
faster by consulting the manual for the version he is using ;-)
> On Sun, Jul 26, 2015 at 1:33 AM, Dawid das <addiw7 at googlemail.com> wrote:
> > Dear Gromacs Experts,
> > I was issued with following minimize.mdp file:
> > ; Minimization of bovine pancreatic trypsin inhibitor
> > title = minimization of BPTI
> > ; this is a comment
> > integrator = l-bfgs ; (other: cg, l-bfgs)
> > emtol = 500 ; convergence criterium- maximum value of
> > force [kJ/(mol*nm)]
> > emstep = 0.01 ; initial step size [nm]
> > nsteps = 2000 ; number of steps
> > nstlist = 1 ; frequency update of neighbour list
> > ns_type = grid ; algorithm of updating neighbour list.
> > seems to be cell list method.
> > nstenergy = 50 ;
> > rlist = 1.0
> > coulombtype = PME
> > rcoulomb = 1.0
> > rvdw = 1.0
> > pbc = xyz
> > my question is what is the default cutoff-scheme here? group or Verlet? I
> > assume there has to be default option because otherwhise nstlist and
> > ns_type will not make sense, won't they?
> > The other question is whether I understand ns_type=grid correctly. Is it
> > cell list method as I commented?
> > Best wishes,
> > Dawid Grabarek
> > --
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