shiny chandy wrote:
hello
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
There are two useful sources of information before posting questions:
1. The mailing list archive.
2. The wiki site (wiki.gromacs.org)
You will find a solution to this problem by searching the archive, as this
question is frequently asked. For further reading, have a look at:
http://wiki.gromacs.org/index.php/blowing_up
-Justin
shiny chandy
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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