[CP2K:3410] Re: ERROR in topology_generate_molecule

[Teodoro Laino]

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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