<a imageanchor="1" href="https://lh3.googleusercontent.com/-dyTmC1pMzY0/WjexEXeyflI/AAAAAAAADfA/-imk0ASHQYkR4Oi3byRMlJUFcoRZA1fGQCLcBGAs/s1600/.png" style="margin-left: 1em; margin-right: 1em;"><img src="https://lh3.googleusercontent.com/-dyTmC1pMzY0/WjexEXeyflI/AAAAAAAADfA/-imk0ASHQYkR4Oi3byRMlJUFcoRZA1fGQCLcBGAs/s320/.png" border="0" style="" width="320" height="292"></a><a imageanchor="1" href="https://lh3.googleusercontent.com/-NEGCu6ANRYs/WjexBaiZkSI/AAAAAAAADe8/pnQvzWDI8q45VJ6yYnXKbCMYXoVsgVuMQCLcBGAs/s1600/cp2k11.png" style="margin-left: 1em; margin-right: 1em;"><img src="https://lh3.googleusercontent.com/-NEGCu6ANRYs/WjexBaiZkSI/AAAAAAAADe8/pnQvzWDI8q45VJ6yYnXKbCMYXoVsgVuMQCLcBGAs/s320/cp2k11.png" border="0" width="301" height="320"></a><div>Hi CP2K group,</div><div> </div>I am trying to create a PSF file for ALOOH surface. I have a particular requirement that the psf file should have connections shown as in left figure.<div> </div><div>I have created the PSF file, but CP2K shows error: </div><div>CP2K requires molecules to be contiguous and we have detected a non * <div> * [ABORT] contiguous one!! In particular a molecule defined from index ( * </div><div> * \___/ 1) to ( 210) contains other molecules, not connected! </div><div> </div><div> </div><div>My PSF file look like this: </div><div> </div><div><div> 256 !NATOM </div><div> 1 14 01 DIAS Al1 YA 0.000000 0.0000 0 </div><div> 2 14 01 DIAS Al2 YA 0.000000 0.0000 0 </div><div> 3 03 01 DIAS Al3 YA 0.000000 0.0000 0 </div><div> 4 03 01 DIAS Al4 YA 0.000000 0.0000 0 </div><div> 5 13 01 DIAS Al5 YA 0.000000 0.0000 0 </div><div> 6 13 01 DIAS Al6 YA 0.000000 0.0000 0 </div><div> 7 02 01 DIAS Al7 YA 0.000000 0.0000 0 </div><div> 8 02 01 DIAS Al8 YA 0.000000 0.0000 0 </div><div> 9 12 01 DIAS Al9 YA 0.000000 0.0000 0 </div><div> 10 12 01 DIAS Al1A YA 0.000000 0.0000 0 </div><div> 11 01 01 DIAS Al1B YA 0.000000 0.0000 0 </div></div><div> </div><div>Questions:</div><div>1) If it is same molecule, then in PSF file should SEGMENT ID should be defined exactly in a row? for instance</div><div> </div><div>which format is correct for CP2K. See SEGMENT ID (second column).. Should each molecule be defined in a row or it can be expressed randomly?</div><div> </div><div><div> 256 !NATOM </div><div> 1 AA 01 DIAS Al1 YA 0.000000 0.0000 0 </div><div> 2 BB 01 DIAS Al4 YA 0.000000 0.0000 0 </div><div> 3 AA 01 DIAS Al3 YA 0.000000 0.0000 0 </div><div> 4 AA 01 DIAS Al2 YA 0.000000 0.0000 0 </div><div> 5 BB 01 DIAS Al5 YA 0.000000 0.0000 0 </div></div><div> </div><div> </div><div><div> 256 !NATOM </div><div> 1 AA 01 DIAS Al1 YA 0.000000 0.0000 0 </div><div> 2 AA 01 DIAS Al2 YA 0.000000 0.0000 0 </div><div> 3 AA 01 DIAS Al3 YA 0.000000 0.0000 0 </div><div> 4 BB 01 DIAS Al4 YA 0.000000 0.0000 0 </div><div> 5 BB 01 DIAS Al5 YA 0.000000 0.0000 0 </div></div><div> </div><div> </div><div>2) In my current ALO(OH), except for the non-hydroxy oxygen everything are connected. I could create PSF connecting all atoms (easier to create for me compared to the PSF separating the non-hydroxy oxygen). Is there any easier way to define non-hydroxy oxygens as separate molecules, so that I can have 1-3 VdW, EI.</div><div> </div><div> </div><div>Please let me know. Attached are my PSF, input and PDB files.</div> <div> </div><div> </div><div> On Saturday, February 14, 2015 at 2:53:48 PM UTC+1, Luca wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">Hi Christian, I have investigated in your problem, Maybe the solution is in the definition of molecule in the PSF file . I have just reproduced your error using a small system. The original PSF created with psfgen for 10 waters and 2 ions (SOD and CLA) does not work in cp2k as it is. 29 !NATOM [..] 26 W1 9 TIP3 H1 HT 0.417000 1.0080 0 27 W1 9 TIP3 H2 HT 0.417000 1.0080 0 28 O1 10 CLA CLA CLA -1.000000 35.4500 0 29 O1 11 SOD SOD SOD 1.000000 22.9898 0 [..] Because, cp2k read info about the molecule from segment definition the error arises from the fact that CLA and SOD have same fragment/segment name, which is "O1". If you change this name in the PSF file, it should be work. 28 O1 10 CLA CLA CLA -1.000000 35.4500 0 29 O2 11 SOD SOD SOD 1.000000 22.9898 0 Good luck, Luca > My apologies. I've reported it now. > > > On 12 Feb 2015 21:47, "Teodoro Laino" <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="gRPU4urLpFYJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">teod...@gmail.com</a>> wrote: > Which tone? If you believe that you have a problem with psfgen > you should report this to the psfgen mailing list. > > > On 12 Feb 2015, at 15:07, Christian Jorgensen > > <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="gRPU4urLpFYJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">chr...@gmail.com</a>> wrote: > > > > Sorry I do not understand why the tone on > > this board is like this. I'm simply asking for help. > > > > > > > > > > > > > > > > > > > > On Thu, Feb 12, 2015 at 7:16 AM, Teodoro Laino > > <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="gRPU4urLpFYJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">teod...@gmail.com</a>> wrote: > > report this to the proper mailing list. > > > > > On 11 Feb 2015, at 23:04, Christian Jorgensen > > > <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="gRPU4urLpFYJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">chr...@gmail.com</a>> wrote: > > > > > > ATOM 49880 SOD SOD I 37 21.151 0.526 > > > -30.628 1.00 0.00 ION NA > > > ATOM 49881 SOD SOD I 38 24.667 -35.051 > > > 19.114 1.00 0.00 ION NA > > > ATOM 49882 SOD SOD I 39 -12.620 2.426 > > > 26.969 1.00 0.00 ION NA > > > ATOM 49883 SOD SOD I 40 -10.705 -33.380 > > > -11.158 1.00 0.00 ION NA > > > ATOM 49884 SOD SOD I 41 -19.491 29.350 > > > -34.679 1.00 0.00 ION NA > > > ATOM 49885 SOD SOD I 42 40.802 -30.866 > > > 10.911 1.00 0.00 ION NA > > > ATOM 49886 SOD SOD I 43 -21.411 -20.389 > > > 17.270 1.00 0.00 ION NA > > > ATOM 49887 SOD SOD I 44 13.100 24.287 > > > 18.857 1.00 0.00 ION NA > > > ATOM 49888 SOD SOD I 45 33.628 30.716 > > > 18.333 1.00 0.00 ION NA > > > ATOM 49889 SOD SOD I 46 14.256 -31.556 > > > -9.097 1.00 0.00 ION NA > > > ATOM 49890 SOD SOD I 47 -1.600 38.825 > > > 28.079 1.00 0.00 ION NA > > > ATOM 49891 SOD SOD I 48 26.911 -9.319 > > > 19.217 1.00 0.00 ION NA > > > ATOM 49892 CLA CLA I 49 -21.849 -29.233 > > > -4.389 1.00 0.00 ION CL > > > ATOM 49893 CLA CLA I 50 -27.778 19.207 > > > -8.907 1.00 0.00 ION CL > > > ATOM 49894 CLA CLA I 51 -1.036 -18.525 > > > -33.557 1.00 0.00 ION CL > > > ATOM 49895 CLA CLA I 52 -37.955 23.751 > > > -9.529 1.00 0.00 ION CL > > > ATOM 49896 CLA CLA I 53 -15.636 -34.005 > > > 12.873 1.00 0.00 ION CL > > > ATOM 49897 CLA CLA I 54 40.122 21.296 > > > -26.349 1.00 0.00 ION CL > > > ATOM 49898 CLA CLA I 55 32.593 -9.101 > > > 17.836 1.00 0.00 ION CL > > > ATOM 49899 CLA CLA I 56 8.168 -24.215 > > > 8.246 1.00 0.00 ION CL > > > ATOM 49900 CLA CLA I 57 -4.530 -32.691 > > > -6.031 1.00 0.00 ION CL > > > ATOM 49901 CLA CLA I 58 -14.998 37.422 > > > 2.603 1.00 0.00 ION CL > > > ATOM 49902 CLA CLA I 59 -22.559 -24.866 > > > -37.160 1.00 0.00 ION CL > > > ATOM 49903 CLA CLA I 60 22.442 -17.653 > > > -37.184 1.00 0.00 ION CL > > > ATOM 49904 CLA CLA I 61 -31.657 0.756 > > > -22.411 1.00 0.00 ION CL > > > ATOM 49905 CLA CLA I 62 -25.707 4.569 > > > 26.200 1.00 0.00 ION CL > > > ATOM 49906 CLA CLA I 63 9.816 21.844 > > > -29.523 1.00 0.00 ION CL > > > ATOM 49907 CLA CLA I 64 20.348 15.655 > > > 31.373 1.00 0.00 ION CL > > > ATOM 49908 CLA CLA I 65 -33.471 28.927 > > > 25.816 1.00 0.00 ION CL > > > ATOM 49909 CLA CLA I 66 -23.076 -36.320 > > > -14.581 1.00 0.00 ION CL > > > ATOM 49910 CLA CLA I 67 11.228 23.055 > > > 26.442 1.00 0.00 ION CL > > > ATOM 49911 CLA CLA I 68 -31.967 -25.220 > > > 12.122 1.00 0.00 ION CL > > > ATOM 49912 CLA CLA I 69 7.122 -32.163 > > > -23.902 1.00 0.00 ION CL > > > ATOM 49913 CLA CLA I 70 -30.542 -17.921 > > > 15.502 1.00 0.00 ION CL > > > ATOM 49914 CLA CLA I 71 -35.163 -32.044 > > > 11.857 1.00 0.00 ION CL > > > ATOM 49915 CLA CLA I 72 -1.340 -18.251 > > > -21.790 1.00 0.00 ION CL > > > > > > > > > > > > > > > In relation to the error > > > > > > > > > > > > > > > 49892 0 > > > Two molecules have been defined as identical > > > molecules but atoms mismatch charges!! > > > 49893 0 > > > Two molecules have been defined as identical > > > molecules but atoms mismatch charges!! > > > 49894 0 > > > Two molecules have been defined as identical > > > molecules but atoms mismatch charges!! > > > 49895 0 > > > Two molecules have been defined as identical > > > molecules but atoms mismatch charges!! > > > 49896 0 > > > Two molecules have been defined as identical > > > molecules but atoms mismatch charges!! > > > 49897 0 > > > Two molecules have been defined as identical > > > molecules but atoms mismatch charges!! > > > " > > > > > > > > > > > > > > > How can this be? I've generated this with the > > > standard PSFGEN / Ionize plugin written > > > for VMD. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Wed, Feb 11, 2015 at 9:14 PM, Christian > > > Jorgensen <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="gRPU4urLpFYJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">chr...@gmail.com</a>> wrote: > > > Hello Dr Laino > > > > > > This is a problem with the ions. The atom > > > indices it is warning about are all > > > chlorine added to achieve electrical > > > neutrality ( in VMD with Psfgen for NAMD) > > > > > > I do not understand because I've used the > > > standard procedure from Psfgen > > > > > > On 11 Feb 2015 20:57, "Teodoro Laino" > > > <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="gRPU4urLpFYJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">teod...@gmail.com</a>> wrote: > > > double check your PSF or PDB.. the > > > error is self-esplicative : there > > > must be two or more molecules that > > > have the same name but have > > > different atom sequence.. > > > > > > > > > the fact your PSF or PDB may work > > > with other codes means only that > > > such codes are not performing > > > tight checks. > > > > > > > > > Teo > > > > > > > On 11 Feb 2015, at 18:51, cjor > > > > <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="gRPU4urLpFYJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">chr...@gmail.com</a>> wrote: > > > > > > > > Hello, > > > > I'm trying to run a QMMM > > > > simulation with CP2K based on a > > > > CHARMM FF MD simulation. > > > > > > > > > > > > I first tried to run MM to see > > > > it works, but I get the > > > > following error: > > > > > > > > > > > > > > > > > > > > " > > > > CP2K| version string: > > > > > > > > CP2K version 2.3 > > > > CP2K| source code revision > > > > number: > > > > 12343 > > > > CP2K| is freely available from > > > > > > > > <a href="http://www.cp2k.org/" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.cp2k.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEfybep2Ix3JOTL9zjRCIb7jDt62g';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.cp2k.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEfybep2Ix3JOTL9zjRCIb7jDt62g';return true;">http://www.cp2k.org/</a> > > > > CP2K| Program compiled at > > > > Thu Feb 28 > > > > 16:12:09 GMT 2013 > > > > CP2K| Program compiled on > > > > > > > > popoca > > > > CP2K| Program compiled for > > > > > > > > Linux-x86-64-gfortran > > > > CP2K| Input file name > > > > > > > > mm.inp > > > > > > > > > > > > GLOBAL| Force Environment > > > > number > > > > 1 > > > > GLOBAL| Basis set file name > > > > BASIS_SET > > > > GLOBAL| Geminal file name > > > > BASIS_GEMINAL > > > > GLOBAL| Potential file name > > > > POTENTIAL > > > > GLOBAL| MM Potential file name > > > > MM_POTENTIAL > > > > GLOBAL| Coordinate file name > > > > > > > > ionized.pdb > > > > GLOBAL| Method name > > > > > > > > CP2K > > > > GLOBAL| Project name > > > > > > > > phd2_md > > > > GLOBAL| Preferred FFT library > > > > FFTSG > > > > GLOBAL| Run type > > > > MD > > > > GLOBAL| All-to-all > > > > communication in single > > > > precision > > > > F > > > > GLOBAL| FFTs using library > > > > dependent lengths > > > > F > > > > GLOBAL| Global print level > > > > > > > > LOW > > > > GLOBAL| Total number of message > > > > passing processes > > > > 1 > > > > GLOBAL| Number of threads for > > > > this process > > > > 1 > > > > GLOBAL| This output is from > > > > process > > > > 0 > > > > > > > > > > > > MEMORY| system memory details > > > > [Kb] > > > > MEMORY| > > > > rank 0 min > > > > max average > > > > MEMORY| MemTotal > > > > 132089732 132089732 > > > > 132089732 132089732 > > > > MEMORY| MemFree > > > > 2537384 2537384 > > > > 2537384 2537384 > > > > MEMORY| Buffers > > > > 407408 407408 > > > > 407408 407408 > > > > MEMORY| Cached > > > > 34948436 34948436 > > > > 34948436 34948436 > > > > MEMORY| Slab > > > > 732060 732060 > > > > 732060 732060 > > > > MEMORY| SReclaimable > > > > 581768 581768 > > > > 581768 581768 > > > > MEMORY| MemLikelyFree > > > > 38474996 38474996 > > > > 38474996 38474996 > > > > > > > > > > > > 49892 0 > > > > Two molecules have been defined > > > > as identical molecules but atoms > > > > mismatch charges!! > > > > 49893 0 > > > > Two molecules have been defined > > > > as identical molecules but atoms > > > > mismatch charges!! > > > > 49894 0 > > > > Two molecules have been defined > > > > as identical molecules but atoms > > > > mismatch charges!! > > > > 49895 0 > > > > Two molecules have been defined > > > > as identical molecules but atoms > > > > mismatch charges!! > > > > 49896 0 > > > > Two molecules have been defined > > > > as identical molecules but atoms > > > > mismatch charges!! > > > > 49897 0 > > > > Two molecules have been defined > > > > as identical molecules but atoms > > > > mismatch charges!! > > > > " > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > I'm calling a PSF and PDF file > > > > that I know works. The error > > > > lies with the parsing of the > > > > ion section (SOD and CLA). > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > My MM input is: > > > > > > > > > > > > &GLOBAL > > > > PRINT_LEVEL LOW > > > > PREFERRED_FFT_LIBRARY FFTSG > > > > PROJECT phd2_md > > > > RUN_TYPE MD > > > > &END GLOBAL > > > > > > > > > > > > &MOTION > > > > &MD > > > > ENSEMBLE NPT_I > > > > STEPS 6000 > > > > TIMESTEP 0.48 > > > > TEMPERATURE 298.0 > > > > &THERMOSTAT > > > > TYPE NOSE > > > > REGION MASSIVE > > > > &NOSE > > > > TIMECON [wavenumber_t] > > > > 1000 > > > > &END NOSE > > > > &END THERMOSTAT > > > > &PRINT > > > > &ENERGY > > > > FILENAME =phd2_md.ener > > > > &EACH > > > > MD 1 > > > > &END EACH > > > > &END ENERGY > > > > &PROGRAM_RUN_INFO > > > > &EACH > > > > MD 1 > > > > &END EACH > > > > &END PROGRAM_RUN_INFO > > > > &END PRINT > > > > &END MD > > > > &PRINT > > > > &TRAJECTORY > > > > FILENAME =<a href="http://phd2_md.xyz" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fphd2_md.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGMn0T7gYW78mQ5S6rphrP-xrJEWQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fphd2_md.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGMn0T7gYW78mQ5S6rphrP-xrJEWQ';return true;">phd2_md.xyz</a> > > > > &EACH > > > > MD 1 > > > > &END EACH > > > > &END TRAJECTORY > > > > &RESTART > > > > FILENAME =phd2_md.restart > > > > BACKUP_COPIES 1 > > > > &EACH > > > > MD 10 > > > > &END EACH > > > > &END RESTART > > > > &RESTART_HISTORY OFF > > > > &END RESTART_HISTORY > > > > &END PRINT > > > > &END MOTION > > > > > > > > > > > > &FORCE_EVAL > > > > METHOD FIST > > > > ! Using > > > > Molecular Mechanics > > > > &MM > > > > &FORCEFIELD > > > > parm_file_name > > > > par_all27_prot_lipid.inp > > > > parmtype CHM > > > > ei_scale14 1.0 > > > > vdw_scale14 1.0 > > > > &SPLINE > > > > emax_spline 1.0 > > > > rcut_nb 12 > > > > &END SPLINE > > > > &END FORCEFIELD > > > > &POISSON > > > > &EWALD > > > > ewald_type SPME > > > > alpha 0.44 > > > > gmax 81 > > > > &END EWALD > > > > &END POISSON > > > > &END MM > > > > > > > > > > > > &SUBSYS > > > > &CELL > > > > abc 80 80 80 > > > > periodic xyz > > > > &END CELL > > > > &KIND H > > > > BASIS_SET DZVP-GTH-BLYP > > > > POTENTIAL GTH-BLYP-q1 > > > > &END KIND > > > > &KIND O > > > > BASIS_SET DZVP-GTH-BLYP > > > > POTENTIAL GTH-BLYP-q6 > > > > &END KIND > > > > &KIND N > > > > BASIS_SET DZVP-GTH-BLYP > > > > POTENTIAL GTH-BLYP-q5 > > > > &END KIND > > > > &KIND C > > > > BASIS_SET DZVP-GTH-BLYP > > > > POTENTIAL GTH-BLYP-q4 > > > > &END KIND > > > > &KIND Fe2 > > > > BASIS_SET > > > > DZVP-MOLOPT-SR-GTH > > > > POTENTIAL > > > > DZVP-MOLOPT-SR-GTH > > > > &END KIND > > > > > > > > > > > > &TOPOLOGY > > > > CONNECTIVITY UPSF > > > > COORDINATE PDB > > > > COORD_FILE_NAME > > > > ionized.pdb > > > > CONN_FILE_NAME > > > > ionized.psf > > > > &END TOPOLOGY > > > > &END SUBSYS > > > > &END FORCE_EVAL > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > 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 > > > > +<a href="javascript:" target="_blank" gdf-obfuscated-mailto="gRPU4urLpFYJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">unsu...@googlegroups.com</a>. > > > > To post to this group, send > > > > email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="gRPU4urLpFYJ" 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