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

[st]

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
y1gao at ucsd.edu
858-534-2027
--------------------------------------------------
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 
>> 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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