[gmx-users] Warning errors

[Tsjerk Wassenaar]

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.

Cheers,

Tsjerk

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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