[gmx-users] Warning errors

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Sep 22 20:22:35 CEST 2005

Hi Hector,

You can safely ignore this. It sometimes marks the start of the system
crashing, where some groups (lysine NH3) start spinning and accumulate
energy in the spin, at a certain moment causing the system to explode. But
in your case the system recovers well from it, it seems.



On 9/22/05, Hector Mtz-Seara <h.seara at qf.ub.es> wrote:
> Dear users,
> I am simulating a monolayer system and after preparation ->
> minimization, at the beginning of the simulation I get the following
> warning:
> Step 1, time 0.002 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.131090 (between atoms 3748 and 3749) rms 0.002769
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> After 5 of them they disappear for the rest of the dynamic. My question
> is if might I be concerned for that or I can Ignore them as they have
> disappeared?.
> Thanks in advance.
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciencesand Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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