[gmx-users] LINCS warnings for bonds that do not exist

[Justin Lemkul]

On 8/2/12 9:57 AM, Christian Blouin wrote:
> My simulation aborts rather quickly because it accumulates too many
> LINCS warning. I checked the various plots and everything seems to be
> stable (temperature, pressure, total energy, etc.). The stderr gives
> me warnings looking like this:
>
> Step 2304252, time 4608.5 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.043352, max 0.606635 (between atoms 150 and 151)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>      150    152   90.0    0.0985   0.1490      0.1000
>      150    151   90.0    0.1314   0.1607      0.1000
>
> The problem I see is that atom 150 and 151 do not even have a bond
> between them (they are the two hydrogens of one water molecule). I
> also get similar warning between 150 and 152, which are not even on
> the same water molecule. I have extensively equilibrated the system as
> I thought that it was the problem originally.
>

If that's true, then something is more fundamentally wrong.  The constraint 
length of 0.1 nm indicates an O-H bond, which makes sense if atom 150 is 
actually an O, making 151 and 152 H atoms.  H-H constraints are possible if 
using the SETTLE algorithm for rigid water, but in this case something seems 
inconsistent.

> Anyone here has an intuition as to why this may happen?
>

LINCS warnings always indicate generic instability in the system.  The only real 
advice is here:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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