[gmx-users] Error while doing energy minimization

Shankar Prasad Kanaujia spk at rishi.serc.iisc.ernet.in
Mon Jun 26 11:28:10 CEST 2006

Dear Gromacs Users,
I am getting problem while minimizing the energy. The following are the 
Back Off! I just backed up ener.edr to ./#ener.edr.2#
Polak-Ribiere Conjugate Gradients:
   Tolerance (Fmax)   =  1.00000e+00
   Number of steps    =        20000
   F-max             =  4.32120e+04 on atom 8841
   F-Norm            =          nan

Back Off! I just backed up traj.trr to ./#traj.trr.2#
Program mdrun, VERSION 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 .. 36 ]
Please report this to the mailing list (gmx-users at gromacs.org)

/* My input file is like this
cpp             = /lib/cpp      ; Preprocessor
constraints     = none          ; Bond types to replace by constraints
include         = -I../top      ; Directories to include in the topology 
define          = -DFLEX_SPC    ; Will tell grompp to include FLEX_SPC 
instead of SPC, necessary for cg

; Parameters describing what to do, when to stop and what to save
integrator      = cg            ; Algorithm (steep = steepest descent 
emtol           = 1             ; Stop minimization when the maximum force 
< 1.0 kJ/mol
emstep          = 0.01          ; Initial step-size [nm]
nstcgsteep      = 1000          ; Frequency of performing 1 steepest 
descent step while doing conjugate gradient
nsteps          = 20000         ; Maximum number of (minimization) steps 
to perform
nstcomm         = 1             ; Frequency for center of mass motion 

nstxout         = 10            ; Frequency to write coordinates to output 
trajectory file
nstvout         = 10            ; Frequency to write velocities to output 
trajectory file
nstlog          = 10            ; frequency to write energies to log file
nstenergy       = 10            ; Write energies to disk every nstenergy 
nstxtcout       = 10            ; Write coordinates to disk every 
nstxtcout steps
xtc_grps        = Protein other         ; Which coordinate group(s) to 
write to disk
energygrps      = Protein other         ; Which energy group(s) to write 
to disk

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist         = 10            ; Frequency to update the neighbor list 
and long range forces
ns_type         = grid          ; Method to determine neighbor list 
(simple, grid)
pbc             = xyz           ; Periodic Boundary Condition (xyz, no)
rlist           = 1.0           ; Cut-off for making neighbor list (short 
range forces)
coulombtype     = PME           ; Treatment of long range electrostatic 
rcoulomb        = 1.2           ; Long-range electrostatic cut-off
epsilon_r       = 1             ; Dielectric Constant
fourierspacing  = 0.15
pme_order       = 4
ewald_rtol      = 1e-5
rvdw            = 3.0           ; long range Van der Waals cut-off

Looking forward for any solutions/suggestions.

Shankar Prasad Kanaujia
Ph.D Student
Bioinformatics Center, Department of SERC
IISc, Bangalore - 12
Mobile: 9845631581

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