[gmx-users] simulation in DPPC lipid bilayer

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 22 13:55:14 CEST 2008

prasun kumar wrote:
> Dear Users
> I am trying to do a simulation in lipid using DPPC12a.pdb.I have done 
> all the necessary changes rewuired.I am using FFGMX force field
> while doing positional restarined step its giving following error:
> 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 .. 125 ]
> But during energy minimization step I got a message that energy 
> minimization converges in 18 steps but dint reach the cuttoff value you 
> specified.
> I am eager to know when a person gets this type of error

When your system is blowing up.  A similar message just hit the list a day or so 
ago (hint: check the archives when you get errors), and I provided some search 
terms and advice there:



> Kindly help me
> Waiting for your invaluable suggestions
> -- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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