Hi Justin,
Thanks for the help!
I browsed the error website (did not know if before) and found that I should
use LINCS constrains instead of bonds for the polymer.
I have changed it and it runs well so far.
Thanks.
Stone Gao
University of California, San Diego
Center of Excellence for Advanced Materials
9500 Gilman Dr.
La Jolla, CA 92093-0416
[email protected]
858-534-2027
--------------------------------------------------
From: "Justin A. Lemkul" <[email protected]>
Sent: Monday, September 14, 2009 5:22 PM
To: "Discussion list for GROMACS users" <[email protected]>
Subject: Re: [gmx-users] hydrogen on N (OPLS_241), zero sigma and epsilon
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:
http://oldwiki.gromacs.org/index.php/blowing_up
http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings
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).
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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_______________________________________________
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