[gmx-users] grompp error

[Diego Enry]

ERROR: 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.

try to "Increase the box size or decrease rlist."  <= as ERROR message suggests




On 10/9/07, pragya chohan <pragyachohan at hotmail.com> wrote:
>
>  hi... i have been trying to do grompp for the following file but am getting
> this error:
>  There were 1 error(s) processing your input
> WARNING 3 [file "popc.top", line 32]:
>   7380 non-matching atom names
>   atom names from popc.top will be used
>   atom names from popc.pdb will be ignored
>  double-checking input for internal consistency...
> ERROR: 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.
> There were 3 warnings
>
>  The grompp command i am using is:
>  grompp -f 7eq_w.mdp -c popc.pdb -p popc.top -o poc.tpr
>
>  the inputs are:
>
>  popc.mdp
>
>  title                = popc128a
> integrator           = md
> define               = -DPOSRES -DFLEX_SPC
> dt                   = 0.002
> nsteps               = 25000
> nstxout              = 500
> ns_type              = grid
> pbc                  = xyz
> constraints          = hbonds
> constraints_algorithm= shake
> coulombtype          = PME
> vdwtype              = cut-off
> rcoloumb             = 1.4
>  Tcoupl               = berendsen
> pcoupl               = berendsen
> tau_t                = 0.1       0.1
> tc_grps              = POPC      SOL
> ref_t                = 300       300
> ref_p                = 1.0
> pcoupltype           = isotropic
> compressibility      = 4.5e-5
> gen_temp             = 300
>
>  popc.top
>
>  #include "ffgmx.itp"
> #include "lipid.itp"
> #include "popc.itp"
>  #ifdef FLEX_SPC
> #include "flexspc.itp"
> #else
> #include "spc.itp"
> #endif
>  #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
>  ; Include generic topology for ions
> #include "ions.itp"
>  #ifdef POSRES
> #include "lipid_posre.itp"
> #endif
>  [ system ]
> ; Name
> Pure DPPC bilayer with 128 lipids and 3655 water molecules
>  [ molecules ]
> ; Compound        #mols
> POPC              128
> SOL               2460
>
>
>
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-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.