[gmx-users] Brownian dynamics]

[David van der Spoel]

On 13 Feb 2002, Michel Fodje wrote:

>I didn't find any clashes or flying atoms/bonds in the configuration. 
>However, I just repeated the process with just the protein and no Zn
>ions and I get a different error message
>
>
>Step 0, time 0 (ps)  LINCS WARNING
>relative constraint deviation after LINCS:
>max 4.942302 (between atoms 3138 and 3139) rms 0.529467
>bonds that rotated more than 30 degrees:
> atom 1 atom 2  angle  previous, current, constraint length
>      1      2   90.0    0.1000   0.1062      0.1000
>      1      3   31.9    0.1000   0.0992      0.1000
>      7      8   90.0    0.1000   0.1245      0.1000
>...
I assume that you did use the output file (confout.gro) from the
minimization to generate your dynamics input?

Further you could check the mdp file for strange options. Turn off
everything like freezing restraining etc. Do also check the temperature
you get (and the one you use for BD). Try normal MD, to see whether it is
your conformation or the algorithm


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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