[CP2K:3408] Re: ERROR in topology_generate_molecule

Teodoro Laino teodor... at gmail.com
Fri Aug 5 12:37:05 CEST 2011


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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