[gmx-users] LINCS WARNING...
spoel at xray.bmc.uu.se
Tue Jul 29 20:33:01 CEST 2003
On Tue, 2003-07-29 at 20:18, Senthil Kandasamy wrote:
> > _____________________________________________
> > 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
> 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?
Maybe there is a strong interaction between the hydrogen and a 1-4 atom?
Otherwise, is the hydrogen solvated or hydrogen bonded in any way?
What's the charge on the hydrogen?
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Dr. David van der Spoel, Dept. of Cell and Molecular Biology
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