[gmx-users] hydrogen on N (OPLS_241), zero sigma and epsilon

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 15 02:22:13 CEST 2009

st wrote:
> Hi There,
> I am very thankful to your help always.
> I am working with a system containing a carbon nanotube, a poly ether 
> (charge -1), and a Na+ in spc water.
> I use OPLSAA for the poly ether, water and Na+.
> The poly ether is connected via a peptide bond (-CO-NH-), and I use 
> OPLS_241 for the hydrogen on N.
> H    1.00800     0.300       A     0.00000e+00  0.00000e+00
> When I simulate the system without water, everything seems moves 
> reseanable.
> When I try to simulate the system within water, mdrun_d gives out error 
> after about 10ps(1fs step), saying:
> "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 .. 432 ]
> "
> with the conserved energy blows to +10^20 and total energy blows to 
> +10^11, suddenly.
> When I check the trajectory, I found that the H on N acts strangely at 
> the blow-up. The N-H bond, which should be around 0.101nm, suddenly goes 
> to ~4nm and the H is out of the box.
> I think this should be the cause of the mdrun failure.
> But I do not know what happened, I can only guess. (everything looks 
> fine before that step)
> What should I do to avoid such blow-ups? Thanks.
> It seems to me that the reason is the H has zero sigma and epsilon, 
> which leads to zero non-bond interactions with all other non-bonded atoms.
> So in the simulation, H could go very near to a nearby big atom by 
> accidence (because it is only controlled by the nearby N, one bond, two 
> angles, and three dihedrals (and two dihe are zeros))
> and then due to the ionic repulsion, the H gets big velocity and is 
> pushed far away.
> I do not know if I am right in this. Please let me know your opinion. 
> Thanks a lot!

The hydrogen atom having a zero value for sigma and epsilon is not the source of 
the problem.  Otherwise, one might expect that any force field with these terms 
would lead to the same problem.  Turns out that most force fields assign zero to 
these parameters for H.

You are experiencing a common problem called "blowing up," which has been 
address countless times on this list.  Consult the following resources:


If you are still having problems, you will have to give a more thorough 
description of what your system is and what you've done to prepare it (including 
.mdp files, if necessary).


> And what should I do to avoid this? All the parameters are from OPLSAA.
> (Plus I see similar things on several H atoms in water molecules, but 
> they work fine with my other systems.)
> Thanks in advance!
> Warm regards,
> Stone Gao
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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