[CP2K:6138] PSF file for huge systems

[Pawel Wityk]

Hi Luca,

I checked my PSF file and I have corrected all errors.
Currently I'm optimizing my system and all seems to work,
I had also errors in angle definition :)

Thanks for help for Luca and Teo

Best regards,
Pawel Wityk 






W dniu czwartek, 19 lutego 2015 12:39:46 UTC+1 użytkownik Luca napisał:
>
> Hi Pavel, 
> it seems that in your psf file there are many errors. 
>
> For example, starting from atoms 31301 the  residue definition is lost: 
>    31299 C    1000 SOL  OW   OW    -0.834000       16.0000           0 
>    31300 C    1000 SOL  HW1  HW     0.417000        1.0080           0 
>    31301 C    1000 SOL  HW2  HW     0.417000        1.0080           0 
>    31302 C    1000 SOL  OW   OW    -0.834000       16.0000           0 
>    31303 C    1000 SOL  HW1  HW     0.417000        1.0080           0 
>    31304 C    1000 SOL  HW2  HW     0.417000        1.0080           0 
> It should be: 
>    31299 C    1000 SOL  OW   OW    -0.834000       16.0000           0 
>    31300 C    1000 SOL  HW1  HW     0.417000        1.0080           0 
>    31301 C    1000 SOL  HW2  HW     0.417000        1.0080           0 
>    31302 C    1001 SOL  OW   OW    -0.834000       16.0000           0 
>    31303 C    1001 SOL  HW1  HW     0.417000        1.0080           0 
>    31304 C    1001 SOL  HW2  HW     0.417000        1.0080           0 
> And so on. 
>   
> At this moment, you are providing a wrong psf file, so, what can you 
> expect from cp2k? 
>   
> Luca 
>
>
>
>
> On Wed, 2015-02-18 at 10:56 -0800, Pawel Wityk wrote: 
> > Dear cp2k users, 
> > 
> > I'm starting my QM/MM calculation, I have .psf file *.pdb file for my 
> > whole system, 
> > the number of groups is larger than 9999 (due to water residues). I 
> > think that I have problem with this high amount of water residues, 
> > while starting cp2k run. 
> > My input file is very small and designed to testing *.psf files. 
> > 
> > 
> > Error message: 
> > 
> > 
>  ************************************************************************** 
> >  *** 19:38:25 ERRORL2 in 
> > *** 
> >  *** topology_connectivity_util:topology_connectivity_pack processor 0 
> > *** 
> >  *** err=-300 condition FAILED at line 651 
> > *** 
> > 
>  ************************************************************************** 
> > 
> > 
> >  ===== Routine Calling Stack ===== 
> > 
> >             7 topology_connectivity_pack_11 
> >             6 topology_connectivity_pack 
> >             5 topology_control 
> >             4 fist_init 
> >             3 fist_create_force_env 
> >             2 qmmm_create_force_env_low 
> >             1 CP2K 
> > 
> > 
> > Please, If anyone could help me I will be glad, 
> > I was trying to do some changes in files but I failed and I am 
> > currently stuck. 
> > 
> > 
> > 
> > My input files, are attached below: 
> > 
> > 
> > Best regards, 
> > Pawel Wityk 
> > University of Gdansk 
> > 
> > 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> > Groups "cp2k" group. 
> > To unsubscribe from this group and stop receiving emails from it, send 
> > an email to cp2k+... at googlegroups.com <javascript:>. 
> > To post to this group, send email to cp... at googlegroups.com 
> <javascript:>. 
> > Visit this group at http://groups.google.com/group/cp2k. 
> > For more options, visit https://groups.google.com/d/optout. 
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20150220/556071fb/attachment.htm>