[gmx-users] mdp options in GROMACS 4.5.5

[Mark Abraham]

Hi,

You almost certainly don't want to use version 4.5.5. It's many years old,
slow and contains many bugs that have been fixed. Get a new version
installed ;-)

Mark

On Tue, 6 Jun 2017 17:49 João Henriques <joao.m.a.henriques at gmail.com>
wrote:

> Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I
> mean, not the integration).
>
> /J
>
> On Tue, Jun 6, 2017 at 5:45 PM, João Henriques <
> joao.m.a.henriques at gmail.com
> > wrote:
>
> > Hi!
> >
> > I'm not sure Verlet was already implemented in GMX 4.5.5, but check the
> > manual for that version (or the closest one).
> >
> > Cheers,
> >
> > /J
> >
> > On Tue, Jun 6, 2017 at 3:27 PM, <mohammad.r0325 at yahoo.com> wrote:
> >
> >> Hi All,
> >> I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp -
> >> used as input into grompp to generate em.tpr
> >> integrator      = steep         ; Algorithm (steep = steepest descent
> >> minimization)
> >> emtol           = 1000.0        ; Stop minimization when the maximum
> >> force < 1000.0 kJ/mol/nm
> >> emstep      = 0.01      ; Energy step size
> >> nsteps          = 50000         ; Maximum number of (minimization) steps
> >> to perform
> >>
> >> ; Parameters describing how to find the neighbors of each atom and how
> to
> >> calculate the interactions
> >> nstlist             = 1             ; Frequency to update the neighbor
> >> list and long range forces
> >> cutoff-scheme   = Verlet
> >> ns_type             = grid              ; Method to determine neighbor
> >> list (simple, grid)
> >> coulombtype         = PME               ; Treatment of long range
> >> electrostatic interactions
> >> rcoulomb            = 1.0               ; Short-range electrostatic
> >> cut-off
> >> rvdw                = 1.0               ; Short-range Van der Waals
> >> cut-off
> >> pbc                     = xyz           ; Periodic Boundary Conditions
> >> (yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the
> error
> >> which said that the cutoff-scheme is not recognized. what should I write
> >> instead of "cutoff-scheme" in this version?
> >> Thanks,Mohammad
> >> --
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