[gmx-users] Cutoff length

[fsaadedi at staffmail.ed.ac.uk]

Interesting? Please specify what you mean by that.

Farid

Quoting Xavier Periole <x.periole at rug.nl>:

> fsaadedi at staffmail.ed.ac.uk wrote:
>
>>
>> Dear Users,
>>
>> I'm running a simulation with a peptide in water but the simulation 
>> crashed after 600ps.
>
> 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
> ----------------------------------
>
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