<p dir="ltr">Hello Dr Laino</p>
<p dir="ltr">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)</p>
<p dir="ltr"> I do not understand because I've used the standard procedure from Psfgen</p>
<div class="gmail_quote">On 11 Feb 2015 20:57, "Teodoro Laino" <<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">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..<div><br></div><div>the fact your PSF or PDB may work with other codes means only that such codes are not performing tight checks.</div><div><br></div><div>Teo</div><div><br><div><blockquote type="cite"><div>On 11 Feb 2015, at 18:51, cjor <<a href="mailto:chri...@gmail.com" target="_blank">chri...@gmail.com</a>> wrote:</div><br><div><div dir="ltr">Hello, <div>I'm trying to run a QMMM simulation with CP2K based on a CHARMM FF MD simulation.</div><div><br></div><div>I first tried to run MM to see it works, but I get the following error:</div><div><br></div><div><br></div><div>"</div><div><div> CP2K| version string: CP2K version 2.3</div><div> CP2K| source code revision number: 12343</div><div> CP2K| is freely available from <a href="http://www.cp2k.org/" target="_blank">http://www.cp2k.org/</a></div><div> CP2K| Program compiled at Thu Feb 28 16:12:09 GMT 2013</div><div> CP2K| Program compiled on popoca</div><div> CP2K| Program compiled for Linux-x86-64-gfortran</div><div> CP2K| Input file name mm.inp</div><div><br></div><div> GLOBAL| Force Environment number 1</div><div> GLOBAL| Basis set file name BASIS_SET</div><div> GLOBAL| Geminal file name BASIS_GEMINAL</div><div> GLOBAL| Potential file name POTENTIAL</div><div> GLOBAL| MM Potential file name MM_POTENTIAL</div><div> GLOBAL| Coordinate file name ionized.pdb</div><div> GLOBAL| Method name CP2K</div><div> GLOBAL| Project name phd2_md</div><div> GLOBAL| Preferred FFT library FFTSG</div><div> GLOBAL| Run type MD</div><div> GLOBAL| All-to-all communication in single precision F</div><div> GLOBAL| FFTs using library dependent lengths F</div><div> GLOBAL| Global print level LOW</div><div> GLOBAL| Total number of message passing processes 1</div><div> GLOBAL| Number of threads for this process 1</div><div> GLOBAL| This output is from process 0</div><div><br></div><div> MEMORY| system memory details [Kb]</div><div> MEMORY| rank 0 min max average</div><div> MEMORY| MemTotal 132089732 132089732 132089732 132089732</div><div> MEMORY| MemFree 2537384 2537384 2537384 2537384</div><div> MEMORY| Buffers 407408 407408 407408 407408</div><div> MEMORY| Cached 34948436 34948436 34948436 34948436</div><div> MEMORY| Slab 732060 732060 732060 732060</div><div> MEMORY| SReclaimable 581768 581768 581768 581768</div><div> MEMORY| MemLikelyFree 38474996 38474996 38474996 38474996</div><div><br></div><div> 49892 0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div> 49893 0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div> 49894 0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div> 49895 0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div> 49896 0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div> 49897 0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div></div><div>"</div><div><br></div><div><br></div><div><br></div><div><br></div><div>I'm calling a PSF and PDF file that I know works. The error lies with the parsing of the </div><div>ion section (SOD and CLA).</div><div><br></div><div><br></div><div><br></div><div><br></div><div>My MM input is:</div><div><br></div><div><div>&GLOBAL</div><div> PRINT_LEVEL LOW</div><div> PREFERRED_FFT_LIBRARY FFTSG</div><div> PROJECT phd2_md</div><div> RUN_TYPE MD</div><div>&END GLOBAL</div><div><br></div><div>&MOTION</div><div> &MD</div><div> ENSEMBLE NPT_I</div><div> STEPS 6000</div><div> TIMESTEP 0.48</div><div> TEMPERATURE 298.0</div><div> &THERMOSTAT</div><div> TYPE NOSE</div><div> REGION MASSIVE</div><div> &NOSE</div><div> TIMECON [wavenumber_t] 1000</div><div> &END NOSE</div><div> &END THERMOSTAT</div><div> &PRINT</div><div> &ENERGY</div><div> FILENAME =phd2_md.ener</div><div> &EACH</div><div> MD 1</div><div> &END EACH</div><div> &END ENERGY</div><div> &PROGRAM_RUN_INFO</div><div> &EACH</div><div> MD 1</div><div> &END EACH</div><div> &END PROGRAM_RUN_INFO</div><div> &END PRINT</div><div> &END MD</div><div> &PRINT</div><div> &TRAJECTORY</div><div> FILENAME =phd2_md.xyz</div><div> &EACH</div><div> MD 1</div><div> &END EACH</div><div> &END TRAJECTORY</div><div> &RESTART</div><div> FILENAME =phd2_md.restart</div><div> BACKUP_COPIES 1</div><div> &EACH</div><div> MD 10</div><div> &END EACH</div><div> &END RESTART</div><div> &RESTART_HISTORY OFF</div><div> &END RESTART_HISTORY</div><div> &END PRINT</div><div>&END MOTION</div><div><br></div><div>&FORCE_EVAL</div><div> METHOD FIST ! Using Molecular Mechanics</div><div> &MM</div><div> &FORCEFIELD</div><div> parm_file_name par_all27_prot_lipid.inp</div><div> parmtype CHM</div><div> ei_scale14 1.0</div><div> vdw_scale14 1.0</div><div> &SPLINE</div><div> emax_spline 1.0</div><div> rcut_nb 12</div><div> &END SPLINE</div><div> &END FORCEFIELD</div><div> &POISSON</div><div> &EWALD</div><div> ewald_type SPME</div><div> alpha 0.44</div><div> gmax 81</div><div> &END EWALD</div><div> &END POISSON</div><div> &END MM</div><div><br></div><div> &SUBSYS</div><div> &CELL</div><div> abc 80 80 80</div><div> periodic xyz</div><div> &END CELL</div><div> &KIND H</div><div> BASIS_SET DZVP-GTH-BLYP</div><div> POTENTIAL GTH-BLYP-q1</div><div> &END KIND</div><div> &KIND O</div><div> BASIS_SET DZVP-GTH-BLYP</div><div> POTENTIAL GTH-BLYP-q6</div><div> &END KIND</div><div> &KIND N</div><div> BASIS_SET DZVP-GTH-BLYP</div><div> POTENTIAL GTH-BLYP-q5</div><div> &END KIND</div><div> &KIND C</div><div> BASIS_SET DZVP-GTH-BLYP</div><div> POTENTIAL GTH-BLYP-q4</div><div> &END KIND</div><div> &KIND Fe2</div><div> BASIS_SET DZVP-MOLOPT-SR-GTH</div><div> POTENTIAL DZVP-MOLOPT-SR-GTH</div><div> &END KIND</div><div><br></div><div> &TOPOLOGY</div><div> CONNECTIVITY UPSF</div><div> COORDINATE PDB</div><div> COORD_FILE_NAME ionized.pdb</div><div> CONN_FILE_NAME ionized.psf</div><div> &END TOPOLOGY</div><div> &END SUBSYS</div><div>&END FORCE_EVAL</div></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div></div><div><br></div>
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