[gmx-users] Re: LINCS Warning using mdrun

Jochen Hub jhub at gwdg.de
Thu Mar 16 17:38:39 CET 2006

Grazia Daminelli wrote:

> Dear Jochen
> what do you mean with:
>> 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
> which term is telling you that there are problems?
> The bonded terms, which are all positive?
> The LJ (SR) which is positive and big?
> and what about the LJ-14 and Coulomb-14?
> I am asking because the energies given by Guarav are not that 
> different from the results I get - and somewhere I have a problem, I 
> know, because my md simulations are not stable (but I can't find out 
> the reason)
> a comment would be highly appreciated
> Grazia

Hi Grazia,

I was wondering if your system converged to a low potential energy and 
low maximum force during energy minimization...


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

More information about the gromacs.org_gmx-users mailing list