[gmx-users] Range checking error

[Ibrahim M. Moustafa]

hi gmx-users,

     I'm a newbie to gromacs. I have done few mutations to my 
structure and wanted to relax the structure by energy minimization.
   The structure has 8 acetate molecules and 297 water molecules + 
461 protein residues. I generated the
parameters for the acetate using PRODRG server and edited the 
protein.top and protein.gro files (generated with removal of the acetate).
Then running the mdrun
   > mdrun -s em.tpr -c after_em.pdb -g em.log &

   gave me the following error:
"Range checking error" source code file: nsgrid.c: line 226
  Variable ci has a value -2147483648. It should have been within [0 ...4320]
Please report this to the mailing list"

    As explained in the error message, the system might have 
collisions or parameter errors that give particles very high 
velocities ending up with some unrealistic coordinates!

   The em.mdp file looks like:
-------------------------------------------------------------------------------------------------------------------------------
title                 = 3Dwt_em
cpp                   = /usr/bin/cpp ; the c pre-processor
define                = -DFLEXIBLE
constraints           = none
integrator            = steep ; for steepest decent; cg (for conjugate grad);
nsteps                = 5000
nstlist               = 5 ; frequency to update the neighbour list ;
rlist                 = 0.9
coulombtype           = PME ; use PME to model electrostatic ;
rcoulomb              = 0.9 ; coulomb cutoff distance ;
rvdw                  = 1.4 ; radius for LJ or Buckingham potential cutoff ;
fourierspacing        = 0.12
fourier_nx            = 0
fourier_ny            = 0
fourier_nz            = 0
pme_order             = 4
ewald_rtol            = 1e-5
optimize_fft          = yes
;
; Energy minimizing step
;
emtol                 = 1000.0 ; the minimiz. converges when max force <1000;
emstep                = 0.01 ; initial step size = 0.01 nm ;

----------------------------------------------------------------------------------------------------------

   The question is how to resolve this error so I can do the minimization??

(Any comments on the keywords of the em.mdp file are welcomed)

   many thanks in advance for your help.

   thanks,
  Ibrahim

Ibrahim M.Moustafa, Ph.D.
Pennsylvania State University
Biochemistry & Molecular Biology Dept.
201 Althouse Lab.
University Park, PA16802

Tel  (814) 863 8703
Fax (814) 865 7927