ERROR in topology_generate_molecule

Nikita vakul... at gmail.com
Mon Aug 8 09:40:25 CEST 2011


Hello Teo!

Thank you very much for your explanation! I've got that! But when the
program writes the charge of the system the calculation stops without
any error. I don't know what is the problem now. Could you please
suggest anything?

Thanks in advance,
Nikita

On 5 авг, 16:59, Teodoro Laino <teodor... at gmail.com> wrote:
> if you have 2 molecules made of atoms A,B and C,D, you can't have:
>
> A
> C
> D
> B
>
> but you need to have them grouped according their molecule. I.e.:
>
> A
> B
> C
> D
>
> hope this is clear.
>
> On Aug 5, 2011, at 2:50 PM, Nikita wrote:
>
>
>
>
>
>
>
> > 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:
>
> >>> 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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