[gmx-users] input file

[Urszula Uciechowska]

Dear gmx users,

I am using 5.0.6 version. After running  the:

grompp -f ions.mdp -c caulob-mod-it_solvated.gro -p caulob-mod-it.top -o
ions.tpr

NOTE 1 [file ions.mdp, line 16]:
  ions.mdp did not specify a value for the .mdp option "cutoff-scheme".
  Probably it was first intended for use with GROMACS before 4.6. In 4.6,
  the Verlet scheme was introduced, but the group scheme was still the
  default. The default is now the Verlet scheme, so you will observe
  different behaviour.


What should I apply in cutoff-scheme ? Please see below my input.file




ions.mpd contains:

; ions.mdp - used as input into grompp to generate ions.tpr
; Parameters describing what to do, when to stop and what to save
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         = 10            ; Frequency to update the neighbor list
and long range forces
ns_type         = grid          ; Method to determine neighbor list
(simple, grid)
rlist           = 1.0           ; Cut-off for making neighbor list (short
range forces)
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)



best
Urszula




University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Kladki 24
80-822 Gdansk
Poland


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http://www.ug.edu.pl/