[gmx-users] Re: LINCS Warning using mdrun

[Jochen Hub]

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
>
> Hi Gaurav,
> what is your stepsize during the simulation? what is constrained? And 
> have you run a minimization before starting the simulation?
> hear from you soon
> Steffen
>
>
> -----------------------------------------------------------------------
> Hi
>
> I used the initial minimization run using grompp and mdrun using 
> steepest descent for 400 steps and 0.002 ps as the step size. The 
> constraints are all-atom.
>
> The following is the output from the log file that was generated after 
> the md.
> Any suggestions?
>
> Thanks
>
> Gaurav
>
> ---------------   mdrun log file output ------------------
>
Better show us the output of your energy minimization. The ouput of your 
md only shows that your sctructure has some serious problem...like your 
box is too small or whatever...

Jochen



-- 
************************************************
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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