[gmx-users] fatal error, running mdrun
David van der Spoel
spoel at xray.bmc.uu.se
Wed Dec 12 09:37:43 CET 2001
On Tue, 11 Dec 2001, Geraudis Mustelier wrote:
>
>Hi all
>Please, someone can explain me what meaning the following error?
>
>Step 0, time 0 (ps) LINCS WARNING
>relative constraint deviation after LINCS:
>max 369.129761 (between atoms 486 and 488) rms 13.426302
>bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 475 477 108.0 0.1330 0.1337 0.1330
> ... .... ... ..... ..... .....
> 3445 3447 92.3 0.1250 0.8337 0.1250
>Wrote pdb files with previous and current coordinates
>Fatal error: Bond deviates more than half its own length
Probably large force due to bad initial structure. Did you minimize?
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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