[gmx-users] Cutoff length

[Xavier Periole]

fsaadedi at staffmail.ed.ac.uk wrote:

>
> Dear Users,
>
> I'm running a simulation with a peptide in water but the simulation 
> crashed after 600ns.

hopefully it is not 600 ns but 600 ps you've run ...
there are many thing to comment on your nput ... check a paper where the 
basics of
the parameters of the force field you use. The cut-off scheme you have 
is pretty interesting.

Best
XAvier

> Fatal error: One of the box vectors has become shorter than twice the 
> cut-off length.
> I include my mdp file to see if there are noticeable errors.
>
>>
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>
>
>
> Any ideas on what may be causing the problem would be much appreciated.
>
> Thank you in advance for your time in this matter.
>
> Farid Sa'adedin
>
> ; PREPROCESSING
> title                  = Bac7alphawater
> cpp                    = /lib/cpp
> include                = -I.
>
> ; RUN CONTROL
> integrator             = md
> tinit                  = 0
> dt                     = 0.002
> nsteps                 = 1500000
> nstcomm                = 10
>
> ; LANGEVIN DYNAMICS
>
> ; ENERGY MINIMIZATION
> emtol                  = 1000.0
> emstep                 = 0.01
> nstcgsteep             = 1000
>
> ; SHELL MOLECULAR DYNAMICS
>
> ; OUTPUT CONTROL
> nstxout                = 10000
> nstvout                = 10000
> nstfout                = 10000
> nstlog                 = 10000
> nstenergy              = 10000
> nstxtcout              = 10000
>
> ; NEIGHBOR SEARCHING
> nstlist                = 1.0
> ns_type                = grid
> pbc                    = xyz
> rlist                  = 1.0
>
> ; ELECTROSTATICS AND VDW
> coulombtype            = Reaction-Field
> rcoulomb               = 1.8
> epsilon_r              = 100.0
> vdwtype                = Cut-off
> rvdw                   = 1.0
> dispcorr               = no
>
> ; TEMPERATURE COUPLING
> tcoupl                 = berendsen
> tau_t                  = 0.1
> ref_t                  = 300
> tc_grps                = System
>
> ; PRESSURE COUPLING
> pcoupl                 = berendsen
> pcoupltype             = isotropic
> tau_p                  = 5.0 5.0 5.0
> compressibility        = 4.5e-5 4.5e-5 4.5e-5
> ref_p                  = 1.0 1.0 1.0
>
> ; SIMULATED ANNEALING
> annealing              = no
> zero_temp_time         = 100
>
> ; VELOCITY GENERATION
> gen_vel                = no
>
>
> ;BONDS
> constraints            = none
> ;constraint_algorithm   = shake
> morse                  = no
>
> ; ENERGY GROUP EXCLUSIONS
>
> ; NMR REFINEMENT
>
> ; FREE ENERGY PERTUBATION
> free_energy             = no
>
> ; NON-EQULIBRIUM MD
>
> ; ELECTRIC FIELDS
>

-- 
----------------------------------
 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   
 Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 
 Tel: +31-503634329
 Fax: +31-503634800
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole
----------------------------------