[gmx-users] input file

[Justin Lemkul]

On 11/2/15 7:27 AM, Urszula Uciechowska wrote:
> 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
>
>

For adding ions it is irrelevant.  See the manual for available options, though 
Verlet is the default going forward as it is superior to the group-based method.

-Justin

>
>
> 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
>
>
> -----------------------------------------
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> http://www.ug.edu.pl/
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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