[gmx-users] problem with LINCS

[Thomas Koller]

Hello!

I have the following problem:

I calculated a stable conformation of two ions of an ionic liquid, e.g. the relative positions of both. I used genbox to replicate the pair structure in the simulation box. After that, I started minimization, volume and pressure equilibration. A few steps after the volume equilibration, I got this message:

Step 2160, time 4.32 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2702.127453, max 65115.246094 (between atoms 130 and 131)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    121    123   91.9    0.1378   0.6015      0.1378
    130    131   90.0    0.1526 9936.7393     0.1526
    ...

I use LINCS with h-angles. 

The whole procedure works when I don't use the conformer pair, but two separate ions inserting randomly in the box. I get no LINCS warning. What can be the problem?

Regards and thanks,
Thomas

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