[gmx-users] MD => system exploding

Justin A. Lemkul jalemkul at vt.edu
Sun Oct 5 17:47:44 CEST 2008

Chih-Ying Lin wrote:
> HI
> When I run MD, my system is exploding.
> And, I found after minimisation, the atoms of my molecule are seperated apart.

That probably suggests that whatever parameters you've applied are not correct.

> The overall charge of my system is +1,  and I put one molecule in the
> gas phase to do the structure test. But, it was already exploding.

What is a "structure test"?  What are you trying to determine?

> Is it hard for a +1 charge molecule to maintain a good shape under MD
> simulation?

Gas-phase charges involve high-energy species (ionized mass spec samples, 
plasma, etc.), so the answer is probably yes.

What is your molecule?  Is it a protein?  If you're using a charged protein in a 
vacuum, the force field you're using may not be valid.


> What are the procedures to test and determine the mistakes I made?
> Thank you
> Lin
> Back Off! I just backed up md.log to ./#md.log.1#
> Getting Loaded...
> Reading file fullmd.tpr, VERSION 3.3.3 (single precision)
> Loaded with Money
> starting mdrun 'azoct'
> 100000 steps,    100.0 ps.
> Warning: 1-4 interaction between 11 and 18 at distance 1.301 which is
> larger than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> step 10, will finish at Sun Oct  5 06:17:20 2008
> -------------------------------------------------------
> Program mdrun, VERSION 3.3.3
> 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 .. 5832 ]
> -------------------------------------------------------
> "She's Not Bad, She's Just Genetically Mean" (Captain Beefheart)
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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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