[gmx-users] LINCS WARNING...

[Senthil Kandasamy]

> _____________________________________________
> Step 400, time 0.8 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.120018 (between atoms 334 and 335) rms 0.002054
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>     333    335   33.8    0.2081   0.2040      0.2000
                                                ^^^^^^
It seems like you are running with constraints = all-angles
LINCS is not good at this. Your options are to use shake for the
constraint algorithm or use constraints = all-bonds
___________________


David, 

I had tried all-bonds and also tried the SHAKE algorithm earlier. They
all seem to crash and the culprit always seems to be that one particular
hydrogen atom. Is there any other way to make it stable? 

Senthil