[CP2K:1035] Re: input coordinates & charges

[Teodoro Laino]

Dear Csilla,

On 13 May 2008, at 14:31, Csilla Varnai wrote:

>
> Dear All,
>
> I am trying to run a program which invokes CP2K at each time step.
> Basically, I will need to run CP2K to calculate the forces during my
> simulations, so I am trying to find the best way to do that.
> I have the atomic coordinates and connectivities stored during the
> run, from which I can create CHARMM format to pass it to CP2K.
>
> I have generated a modified forcefield file of the original
> distribution of CHARMM from the www.charmm.org home page to have a 1-
> to-1 mapping between the atomic types and atomic charges. Having
> revised the way of generating the modified forcefield I have a
> forcefield of reasonable size, and the forcefield can be read by CP2K
> fine. I seem to have no problem with the forcefield any longer, thanks
> for the help!
>
> I thought of relying on the internal topology builder of CP2K.
> But I am getting the following error message with the default
> BONDLENGTH_MAX = 3 Angstroms:
>
>      GENERATE| ERROR in connectivity generation!
>      GENERATE| The THRESHOLD to select possible bonds is larger than
> the max. bondlength
>      GENERATE| used to build the neighbors lists. Increase the
> BONDLENGTH_MAX parameter
>      GENERATE| Present THRESHOLD (   7.233872 ).  Present
> BONDLENGTH_MAX (   5.669178 )
>
>
> Why does it say 5.669178 instead of 6? Is its unit bohr?

3/0.529177
5.66918063332306581729
It's in bohr..

> If I increase the BONDLENGTH_MAX, it does not help. If I set 4.5
> Angstroms then I am getting the following:
>
>
>
>     GENERATE|  Preliminary Number of Bonds
> generated:                         15757
>
>      GENERATE| WARNING in connectivity generation!
>      GENERATE| Two molecules/residues named (HSE) have different
> number of atoms.
>      GENERATE| Molecule starting at position (238) has Nr. <4> of  
> atoms.
>      GENERATE| while the other same molecules have Nr. <11> of atoms!
>      GENERATE| Increasing bondparm_factor by 1.05.. An error was found
> in the generated
>      GENERATE| connectivity. Retry...
>      GENERATE| Present value of BONDPARM_FACTOR (   1.155000 ).
>      ...
>
>      GENERATE| ERROR in connectivity generation!
>      GENERATE| The THRESHOLD to select possible bonds is bigger than
> the MAX bondlength
>      GENERATE| used to build the neighbors lists. Increase the
> BONDLENGTH_MAX patameter
>      GENERATE| Present THRESHOLD (   8.792816 ).  Present
> BONDLENGTH_MAX (   8.503768 )
>
>
> Can the hydrogen bonds cause problems in this case?

Most of the times yes but these errors may appear also because the  
values of the parameters
in the input files are totally wrong.. The construction of the  
topology can be very hard and difficult and requires some
idea of the bond presents and how to catch them properly...
If you want to use the internal topology generator you've to play  
with the parameter of the &GENERATE section.
(In this case the calue of 4.5 it's extremely large!!)

Otherwise I would suggest you to provide a PSF.

Cheers
Teo