[gmx-users] requested for GROMACS package

[Justin A. Lemkul]

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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