[gmx-users] hydrogen on N (OPLS_241), zero sigma and epsilon
y1gao at ucsd.edu
Tue Sep 15 20:45:36 CEST 2009
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.
University of California, San Diego
Center of Excellence for Advanced Materials
9500 Gilman Dr.
La Jolla, CA 92093-0416
y1gao at ucsd.edu
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Sent: Monday, September 14, 2009 5:22 PM
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
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
>> 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
>> 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
> gmx-users mailing list gmx-users at gromacs.org
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