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

st y1gao at ucsd.edu
Tue Sep 15 01:51:01 CEST 2009

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, 

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!
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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