ERROR in topology_generate_molecule

[Nikita]

I'm not sure I understand it clearly. Could you please explain what
does it mean?

Thank you in advance,
Nikita

On Aug 5, 2:37 pm, Teodoro Laino <teodor... at gmail.com> wrote:
> cp2k requires atoms in the same molecule to be contiguous: which I think is also a reasonable assumption.
>
> Teo
>
> On Aug 5, 2011, at 12:32 PM, Nikita wrote:
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>
> > Thank you for your reply!
> > But the thing is it works ok in namd.
> > Thnak you in advance,
> > Nikita
>
> > On 5 авг, 13:53, Teodoro Laino <teodor... at gmail.com> wrote:
> >> Very probably your PSF is fault.
>
> >> You have two options (actually only 1 if you need a topology):
>
> >> 1) fix your psf (keeping in mind that cp2k requires atoms in the same molecule to be contiguous)
>
> >> OR
>
> >> 2) if you do NOT need a topology just read the pdb and connectivity OFF.
>
> >> Teo
>
> >> On Aug 5, 2011, at 11:45 AM, Nikita wrote:
>
> >>> Dear CP2K users and developers,
> >>> I'm trying to run a MM simulation on a quartz surface. I've checked
> >>> carefully my input file, but I can't find the solution to this error:
>
> >>> *** Detected a non contiguous molecule!! Too late at this stage  ***
> >>> *** everything should be already ordered! Try with the keyword   ***
> >>> *** reordering.. It may help!                                    ***
>
> >>> I'm using x-plor psf and a pdb file.
> >>> I've also tried to use the REORDER keyword but it does not work.
>
> >>> Could you please suggest me how to overcome this problem.
>
> >>> Thank you very much in advance,
> >>> Nikita
>
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