[gmx-users] Default cut-off scheme.

[Dawid das]

Actually, I am working with Gromacs 4.6.7, but thank you for a tip ;).
I forgot about the actual manual.

All the best,

Dawid Grabarek

2015-07-25 23:44 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:

> 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 ;-)
>
> Mark
>
>
> > 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.
> > It
> > > 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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