[gmx-users] LINCS warning

[Anton Feenstra]

Lakshmi Padmavathi wrote:
> Dear Gromacs users,
> 
> I made the MD simulations with distance restraints between 100, 101, 168 and 
> 226. i am getting this following warning. is it too serious? can i continue 
> or not.? i hope any of you could help me.
> 
> thank you in advance
> 
> Step 46324, time 92.648 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.005035 (between atoms 100 and 102) rms 0.000117
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>     100    101   45.4    0.1091   0.1095      0.1090

It depends what type of atoms these are, and if they are anywhere
near a significant location in your system of interest. I'd suppose
they are, since you have distance restraints connected to them.

Generally speaking, a Lincs Warning is *serious*. It means a bond
(e.g. N-H, C-O) and the corresponding atom(s) have rotated for more
than 30 degrees, which means you are far from a step size that would
ensure energy conservation. Having said that, I have often ignored
them, for example if it is a solvent-exposed -NH3 group, while I am
only interested in the enzym active site in the interior of the
protein. It also depends if the warning is persistent. I see them
often during the first 10's of ps, but if they disappear quickly
and are far from the important areas, I feel it safe to ignore.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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