[gmx-users] grompp error

[Dallas Warren]

My guess would be that when you thought ran it with the increased box
size coordinate file, you actually used the original coordinate file.

FYI http://www.gromacs.org/Documentation/Errors#The_cut-off_length_is_longer_than_half_the_shortest_box_vector_or_longer_than_the_smallest_box_diagonal_element._Increase_the_box_size_or_decrease_rlist
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 16 October 2017 at 12:22, Amali Guruge <amaligg2010 at gmail.com> wrote:
> Dear Gromacs users,
>
> I got the following error when I tried to run grompp.
> ERROR 1 [file system.top, line 18]:
>   ERROR: One of the box lengths is smaller than twice the cut-off length.
>   Increase the box size or decrease rlist
>
> I increased the box size and re-tried to run grompp,but it didn't work. The
> box size is 20*20*20 nm3. mdp file options are shown in below. Could you
> please anyone help me to solve this problem.
>
> Thank you.
>
> ; Define can be used to control processes
> define          = -DFLEXIBLE
>
> ; Parameters describing what to do, when to stop and what to save
> integrator    = steep        ; Algorithm (steep = steepest descent
> minimization)
> emtol        = 1.0        ; Stop minimization when the maximum force < 1.0
> kJ/mol
> nsteps        = 200        ; Maximum number of (minimization) steps to
> perform
> nstenergy    = 10        ; Write energies to disk every nstenergy steps
> nstcalcenergy    = 10        ; Calculate energy every step
> energygrps    = System    ; Which energy group(s) to write to disk
> nstxout               = 100  ; Frequency of writing to .trr file
>
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> cutoff-scheme   = Verlet
> ns_type        = simple    ; Method to determine neighbor list (simple,
> grid)
> coulombtype    = cut-off    ; Treatment of long range electrostatic
> interactions
> rcoulomb    = 1.0        ; long range electrostatic cut-off
> rvdw        = 1.0        ; long range Van der Waals cut-off
> constraints    = none        ; Bond types to replace by constraints
> pbc        = xyz            ; Periodic Boundary Conditions (yes/no)
> --
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