Thomas Koller wrote:
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?
Hard to say. What does the trajectory show? How successful was energy
minimization, and what were your criteria? What's in your .mdp file?
Additional troubleshooting points can be found here:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
-Justin
Regards and thanks,
Thomas
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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