[gmx-users] Minimize error

[Ana Carolina Sodero]

Hi!

I'm trying to minimize a protein into the box filled with solvent. 
I converted the pdb file into gro file, constructed a triclinic box (volume of ~337 nm3) and filled with 9696 water molecules. I performed the minimization with 150000 steps, using steepest descent integrator (mdp file enclosed).

title                 =  Yo
cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints       =  none
integrator         =  steep
emtol               =  0.0001
emstep             =  0.1
nstcgsteep        =  100
nsteps              =  150000
nstcomm          =  1
nstxout             =  100
nstvout             =  100
nstfout              =  0
nstlog               =  100
nstenergy          =  100
nstlist               =  10
ns_type             =  grid
coulombtype      =  PME
rlist                   =  0.9
rcoulomb           =  0.9
rvdw                 =  0.9
pme_order         =  4
; Berendsen temperature coupling is on in four groups
Tcoupl              =  no
; Isotropic pressure coupling is now on
Pcoupl              =  no


For this particular simulation, the minimization process genarates an error message:

Getting Loaded...
Reading file sj2_steep.tpr, VERSION 3.3.3 (single precision)
Loaded with Money

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e-04
   Number of steps    =       150000
Step=    0, Dmax= 1.0e-01 nm, Epot= -2.43719e+05 Fmax= 1.22008e+06, atom= 4686
Wrote pdb files with previous and current coordinates
Step=    1, Dmax= 1.0e-01 nm, Epot= -2.74902e+05 Fmax= 1.82701e+05, atom= 14670

Back Off! I just backed up step1.pdb to ./#step1.pdb.1#
Wrote pdb files with previous and current coordinates
Step=    2, Dmax= 1.2e-01 nm, Epot= -3.14226e+05 Fmax= 1.01056e+05, atom= 14672

Back Off! I just backed up step2.pdb to ./#step2.pdb.1#
Wrote pdb files with previous and current coordinates
Step=    3, Dmax= 1.4e-01 nm, Epot= -3.45258e+05 Fmax= 8.00739e+04, atom= 18315

Back Off! I just backed up step3.pdb to ./#step3.pdb.1#
Wrote pdb files with previous and current coordinates
Step=    4, Dmax= 1.7e-01 nm, Epot= -3.66329e+05 Fmax= 5.66550e+04, atom= 10626

Back Off! I just backed up step4.pdb to ./#step4.pdb.1#
Wrote pdb files with previous and current coordinates
Step=    5, Dmax= 2.1e-01 nm, Epot= -1.37090e+23 Fmax=         inf, atom= 5356

-------------------------------------------------------
Program mdrun, VERSION 3.3.3
Source code file: nsgrid.c, line: 226

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 3240 ]

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

Does anyone know how can I fix it???

Best Regard!

Ana Carolina

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