<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">the bond must be in the PSF (just fix it by hand). CP2K evaluates the bond directly within minimum image convention.<div>Teo</div><div> <div><div>On Aug 23, 2011, at 12:04 PM, Nikita Vakula wrote:</div> <blockquote type="cite">Hello Teo! Thank you very much for your prompt reply! Yes there should be a bond between them but it is formed only when the unit cell is replicated. And then the thing is: how to set this bond between two atoms which are located in different unit cells? I couldn't find any useful suggestions or variants to realise it? Could you please tell me how to set connection between these atoms? Thank you very much in advance, Nikita <div class="gmail_quote">2011/8/23 Teodoro Laino <<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a>> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"> Particles 72 and 36 are at approx 1.63 angstrom. They must be bond-connected and your PSF does not include this bond. Check it! If there is no bond between them then there are all good reasons to abort the calculation: they would fly in opposite directions in few fs.. (too close!) Teo <div><div></div><div class="h5"> On Aug 23, 2011, at 11:43 AM, Nikita wrote: > Dear CP2K users and developers, > I'm trying to do some MD calculations but all my attempts have > finished with the following error: > **************** > WARNING| Particles: 72 36 at distance [au]: 3.08384421 > less than: 4.43366249; increase EMAX_SPLINE. > * > *** ERROR in build_neighbor_lists *** > * > *** GEOMETRY wrong or EMAX_SPLINE too small! *** > **************** > I've checked my pdb and it seems to be ok. Particles that were pointed > out by the program are at the opposite sides of the unit cell. After > replication this unit cell the distance between these two atoms is > also ok. This geometry was taken from the dft calculation that had > ended up normally. Could anybody tell me what's wrong? Input is below. > > Thank you in advance, > Nikita > > &FORCE_EVAL > METHOD FIST > &MM > &FORCEFIELD > PARMTYPE CHM > PARM_FILE_NAME ./par_silicates.inp > IGNORE_MISSING_CRITICAL_PARAMS .true. > &END FORCEFIELD > &POISSON > &EWALD > EWALD_TYPE SPME > # ALPHA .44 > GMAX 60 60 60 > &END EWALD > &END POISSON > &END MM > &SUBSYS > &CELL > A 19.65120000 0.00000000 0.00000000 > B 0.00000000 17.04684000 0.00000000 > C 0.00000000 0.00000000 30.00000000 > ALPHA_BETA_GAMMA 90.0 90.0 90.0 > PERIODIC XY > &END CELL > &TOPOLOGY > CONN_FILE_NAME ./surf1.psf > CONNECTIVITY UPSF > COORD_FILE_NAME ./surf1.pdb > COORDINATE PDB > &END TOPOLOGY > &END SUBSYS > &END FORCE_EVAL > &GLOBAL > PRINT_LEVEL medium > PROJECT surf_MD > RUN_TYPE MD > &END GLOBAL > &MOTION > &MD > ENSEMBLE NVT > TEMPERATURE 573.15 > STEPS 20000 > TIMESTEP 0.5 > &THERMOSTAT > &NOSE > # LENGTH 3 > # YOSHIDA 3 > # TIMECON 100.0 > # MTS 2 > &END NOSE > &END > &END MD > &END MOTION > > -- > You received this message because you are subscribed to the Google Groups "cp2k" group. > To post to this group, send email to <a href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a>. > To unsubscribe from this group, send email to <a href="mailto:cp2k%2Bun...@googlegroups.com">cp2k+uns...@googlegroups.com</a>. > For more options, visit this group at <a href="http://groups.google.com/group/cp2k?hl=en" target="_blank">http://groups.google.com/group/cp2k?hl=en</a>. > -- You received this message because you are subscribed to the Google Groups "cp2k" group. To post to this group, send email to <a href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a>. To unsubscribe from this group, send email to <a href="mailto:cp2k%2Bun...@googlegroups.com">cp2k+uns...@googlegroups.com</a>. For more options, visit this group at <a href="http://groups.google.com/group/cp2k?hl=en" target="_blank">http://groups.google.com/group/cp2k?hl=en</a>. </div></div></blockquote></div> <div> </div> -- You received this message because you are subscribed to the Google Groups "cp2k" group. To post to this group, send email to <a href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a>. To unsubscribe from this group, send email to <a href="mailto:cp2k+uns...@googlegroups.com">cp2k+uns...@googlegroups.com</a>. For more options, visit this group at <a href="http://groups.google.com/group/cp2k?hl=en">http://groups.google.com/group/cp2k?hl=en</a>. </blockquote></div> </div></body></html>