[gmx-users] fatal error, running mdrun

[David van der Spoel]

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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++