[gmx-users] LINCS Warning using mdrun

Jochen Hub jhub at gwdg.de
Tue Mar 14 15:22:52 CET 2006

Gaurav Chopra wrote:

> Hi
> I get the following error when using mdrun for a protein in solution. 
> I have checked the structure and everything looks fine to me. Could 
> you suggested anything else I could do. 

How did you energy minimze your structure? What was the output of mdrun 
during energy minization, especially the last line with Fmax, Epot etc.?

I should look like this:

Step=   48, Dmax= 1.1e-02 nm, Epot= -1.45545e+06 Fmax= 5.58480e+05, 
atom= 78754
Step=   49, Dmax= 1.4e-02 nm, Epot= -1.45551e+06 Fmax= 8.80803e+03, 
atom= 13032
Step=   50, Dmax= 1.7e-02 nm, Epot= -1.45574e+06 Fmax= 1.60758e+04, 
atom= 13032


Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de

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