[gmx-users] Re: LINCS Warning using mdrun

[Jochen Hub]

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



-- 
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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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