[gmx-users] requested for GROMACS package

shiny chandy shinychandy at gmail.com
Tue Aug 12 12:33:56 CEST 2008

I am working with protien 1PGB having 56 amino acids (practical tutorial
from GROMACS web site) for its simulation using the flexilbe water.
the commands that i have run are :

At later stsges of MD simulations ( i.e after position restrained MD), I
have been getting few errors which are as follow:
*./grompp –f run.mdp –p topol.top –c pr.gro –o run.tpr*
 followed by
*./mdrun –v –deffnm run*
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 .. 486 ]
this is my *run.mdp* file
integrator  = md
nsteps      = 5000
dt          = 0.002
nstlist     = 10
rlist       = 1.0
coulombtype = pme
rcoulomb    = 1.0
vdw-type    = cut-off
rvdw        = 1.0
tcoupl      = Berendsen
tc-grps     = protein non-protein
tau-t       = 0.1 0.1
ref-t       = 298 298
nstxout     = 1000
nstvout     = 1000
nstxtcout   = 100
nstenergy   = 100
what can i do in order to get rid of this error.
your help is kindly needed. In case if i need to give more  information,
please write back

shiny chandy
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