<div dir="ltr">Hi Marcella, <div> Thank you for your quick response. Meanwhile I implemented your advice and replaced my "xyz" type coordinate file with a "pdb" file, with CONNEC information. But apparently CP2K is unable to read the connectivity information from there. So I defined a "PSF" file for the molecule myself and tried reading the connectivity information from there. However I'm getting the error:+ ``` PSF_INFO| CMA :: Unimplemented keyword in CP2K PSF/UPSF format!``` Here is my PDB and PSF files. Could you please help me understand what is going wrong? Is there any alternate ways to define the connectivity for artificial molecules like these? I appreciate your time and help. 1. C5_20.pdb ``` HEADER TITLE Built with Packmol REMARK Packmol generated pdb file REMARK Home-Page: <a href="http://m3g.iqm.unicamp.br/packmol">http://m3g.iqm.unicamp.br/packmol</a> REMARK ATOM 1 C1 CC AA 1 3.763 1.559 -0.001 1.00 0.00 C ATOM 2 C2 CC AA 1 4.432 1.969 0.619 1.00 0.00 C ATOM 3 C3 CC AA 1 5.101 2.380 1.238 1.00 0.00 C ATOM 4 C4 CC AA 1 5.770 2.791 1.858 1.00 0.00 C ATOM 5 C5 CC AA 1 6.439 3.202 2.477 1.00 0.00 C ATOM 6 C1 CC AA 2 7.024 10.035 5.233 1.00 0.00 C ATOM 7 C2 CC AA 2 6.590 9.963 4.335 1.00 0.00 C ATOM 8 C3 CC AA 2 6.156 9.890 3.437 1.00 0.00 C ATOM 9 C4 CC AA 2 5.722 9.817 2.539 1.00 0.00 C ATOM 10 C5 CC AA 2 5.288 9.744 1.641 1.00 0.00 C ATOM 11 C1 CC AA 3 10.002 6.551 9.985 1.00 0.00 C ATOM 12 C2 CC AA 3 9.995 5.677 9.500 1.00 0.00 C ATOM 13 C3 CC AA 3 9.989 4.802 9.014 1.00 0.00 C ATOM 14 C4 CC AA 3 9.983 3.928 8.529 1.00 0.00 C ATOM 15 C5 CC AA 3 9.977 3.053 8.044 1.00 0.00 C ATOM 16 C1 CC AA 4 3.604 2.706 9.741 1.00 0.00 C ATOM 17 C2 CC AA 4 2.835 3.343 9.802 1.00 0.00 C ATOM 18 C3 CC AA 4 2.067 3.980 9.863 1.00 0.00 C ATOM 19 C4 CC AA 4 1.298 4.616 9.925 1.00 0.00 C ATOM 20 C5 CC AA 4 0.529 5.253 9.986 1.00 0.00 C CONECT 1 2 CONECT 2 1 3 CONECT 3 2 4 CONECT 4 3 5 CONECT 5 4 CONECT 6 7 CONECT 7 6 8 CONECT 8 7 9 CONECT 9 8 10 CONECT 10 9 CONECT 11 12 CONECT 12 11 13 CONECT 13 12 14 CONECT 14 13 15 CONECT 15 14 CONECT 16 17 CONECT 17 16 18 CONECT 18 17 19 CONECT 19 18 20 CONECT 20 19 END ``` 2. C5_molecule.psf ``` PSF CMAP 1 !NTITLE 5 !NATOM 1 MOL 1 CC C1 C 0.000000 12.0110 0 2 MOL 1 CC C2 C 0.000000 12.0110 0 3 MOL 1 CC C3 C 0.000000 12.0110 0 4 MOL 1 CC C4 C 0.000000 12.0110 0 5 MOL 1 CC C5 C 0.000000 12.0110 0 4 !NBOND: bonds 1 2 2 3 3 4 4 5 3 !NTHETA: angles 1 2 3 2 3 4 3 4 5 2 !NPHI: dihedrals 1 2 3 4 2 3 4 5 0 !NIMPHI: impropers 0 !NCRTERM: cross-terms ``` 3. Input file ``` &GLOBAL PRINT_LEVEL HIGH ! Low verbosity PROJECT MD_simulation RUN_TYPE MD &END GLOBAL &MOTION &MD ENSEMBLE NVT ! Constant volume TEMPERATURE 420 TIMESTEP 4.0 ! 4 fs STEPS 100000 ! &THERMOSTAT TYPE CSVR &END THERMOSTAT &PRINT &ENERGY &EACH MD 25 ! 25*TIMESTEP &END EACH &END ENERGY &PROGRAM_RUN_INFO &EACH MD 25 ! 25*TIMESTEP &END EACH &END PROGRAM_RUN_INFO &END PRINT &END MD &PRINT &TRAJECTORY &EACH MD 25 ! 25*TIMESTEP &END EACH &END TRAJECTORY &END PRINT &END MOTION &FORCE_EVAL METHOD FIST &MM &FORCEFIELD DO_ELECTROSTATICS F ! Ignore electrostatics (potential from QC) IGNORE_MISSING_CRITICAL_PARAMS T ! Ignore bonded parameters (potential from QC) &SPLINE EMAX_SPLINE 5000 EPS_SPLINE 1.00000000E-8 ! Increase spline accuracy &END SPLINE &BOND ATOMS C C K 900.0 KIND HARMONIC R0 1.0 &END BOND &BEND ATOMS C C C KIND HARMONIC K [rad^-2kcalmol] 1100.0 THETA0 [deg] 180 &END BEND &CHARGE ATOM C CHARGE 0 &END CHARGE &NONBONDED &LENNARD-JONES atoms C C EPSILON 0.08 SIGMA 3.1507 RCUT 11.4 RMIN 1.0 &END LENNARD-JONES &END NONBONDED &END FORCEFIELD &POISSON PERIODIC NONE &EWALD EWALD_TYPE NONE &END EWALD &END POISSON &END MM &SUBSYS &CELL PERIODIC XYZ ABC 30 30 30 &END CELL &TOPOLOGY COORD_FILE_FORMAT pdb COORD_FILE_NAME C5_20.pdb CONN_FILE_FORMAT PSF CONN_FILE_NAME C5_molecule.psf &END TOPOLOGY &END SUBSYS STRESS_TENSOR NUMERICAL &END FORCE_EVAL ``` </div></div> <div class="gmail_quote gmail_quote_container"><div dir="ltr" class="gmail_attr">On Tue, Feb 18, 2025 at 4:34 PM Marcella Iannuzzi <<a href="mailto:marci.akira@gmail.com">marci.akira@gmail.com</a>> wrote: </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi <div> </div><div>If that is the problem , a straightforward way would be to pass the connectivity information through a connectivity file. </div><div>The connectivity generated by CP2K can also be tuned from <ul><li style="color:rgb(64,64,64);font-family:Lato,proxima-nova,"Helvetica Neue",Arial,sans-serif;font-size:16px;box-sizing:border-box;list-style:none;display:inline-block;padding-top:5px"><a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL.html" style="box-sizing:border-box;color:rgb(155,89,182)" target="_blank">FORCE_EVAL</a></li></ul> <ul><li style="color:rgb(64,64,64);font-family:Lato,proxima-nova,"Helvetica Neue",Arial,sans-serif;font-size:16px;box-sizing:border-box;list-style:none;display:inline-block;padding-top:5px"><a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS.html" style="box-sizing:border-box;color:rgb(155,89,182)" target="_blank">SUBSYS</a></li></ul> <ul><li style="color:rgb(64,64,64);font-family:Lato,proxima-nova,"Helvetica Neue",Arial,sans-serif;font-size:16px;box-sizing:border-box;list-style:none;display:inline-block;padding-top:5px"><a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/TOPOLOGY.html" style="box-sizing:border-box;color:rgb(155,89,182)" target="_blank">TOPOLOGY</a></li></ul> <ul><li style="color:rgb(64,64,64);font-family:Lato,proxima-nova,"Helvetica Neue",Arial,sans-serif;font-size:16px;box-sizing:border-box;list-style:none;display:inline-block;padding-top:5px">GENERATE</li></ul></div><div> </div><div>Coordinates passed in PDB format, where molecule name and molecule number are specified, might also work. </div><div> </div><div>Regards</div><div>Marcella</div><div> </div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, February 18, 2025 at 3:06:02 PM UTC+1 Planck wrote: </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi, I am trying to simulate molecular dynamics for a hypothetical chain of carbon atoms (this is a minimum working example designed to illustrate a larger issue I am facing). Each molecule consists of 5 carbon atoms, and my simulation contains 4 such molecules. ``` 20 #Built with Packmol C 264.316076 114.220486 50.721755 C 264.392382 114.277533 50.950866 C 264.525927 114.377373 51.351839 C 264.659472 114.477213 51.752813 C 264.735777 114.534260 51.981923 C 327.956067 237.050267 49.303207 C 327.861562 237.033691 49.074379 C 327.696165 237.004681 48.673899 C 327.530769 236.975671 48.273418 C 327.436264 236.959095 48.044590 C 433.879103 142.141879 115.467902 C 433.814625 141.918476 115.381286 C 433.701780 141.527492 115.229696 C 433.588936 141.136507 115.078106 C 433.524458 140.913105 114.991490 C 234.869472 121.984410 116.856352 C 234.879704 121.977472 116.608530 C 234.897610 121.965330 116.174809 C 234.915516 121.953188 115.741088 C 234.925748 121.946251 115.493266 ``` I have defined a Lennard-Jones potential between the carbon atoms. My input file looks like this: ``` &GLOBAL PRINT_LEVEL HIGH ! Low verbosity PROJECT MD_simulation RUN_TYPE MD &END GLOBAL &MOTION &MD ENSEMBLE NVT ! Constant volume TEMPERATURE 420 TIMESTEP 4.0 ! 4 fs STEPS 100000 ! &THERMOSTAT TYPE CSVR &END THERMOSTAT &PRINT &ENERGY &EACH MD 25 ! 25*TIMESTEP &END EACH &END ENERGY &PROGRAM_RUN_INFO &EACH MD 25 ! 25*TIMESTEP &END EACH &END PROGRAM_RUN_INFO &END PRINT &END MD &PRINT &TRAJECTORY &EACH MD 25 ! 25*TIMESTEP &END EACH &END TRAJECTORY &END PRINT &END MOTION &FORCE_EVAL METHOD FIST &MM &FORCEFIELD DO_ELECTROSTATICS F ! Ignore electrostatics (potential from QC) IGNORE_MISSING_CRITICAL_PARAMS T ! Ignore bonded parameters (potential from QC) &SPLINE EMAX_SPLINE 5000 EPS_SPLINE 1.00000000E-8 ! Increase spline accuracy &END SPLINE &NONBONDED &LENNARD-JONES atoms C C EPSILON [kcalmol] 0.08 SIGMA [angstrom] 3.1507 RCUT [angstrom] 11.4 RMIN 1.0 &END LENNARD-JONES &END NONBONDED &END FORCEFIELD &POISSON PERIODIC NONE &EWALD EWALD_TYPE NONE &END EWALD &END POISSON &END MM &SUBSYS &CELL PERIODIC XYZ ABC 800 800 800 &END CELL &TOPOLOGY COORD_FILE_FORMAT XYZ COORD_FILE_NAME C5_20.xyz &END TOPOLOGY &END SUBSYS STRESS_TENSOR NUMERICAL &END FORCE_EVAL ``` but when I run the simulation, I encounter the following error: ``` SPLINE_INFO| Generating 1 splines for NONBONDED interactions Due to 1 different atomic kinds ******************************************************************************* * ___ * * / \ * * [ABORT] SPLINE_INFO| Number of points: 2346797 obtained accuracy 43.1289 * * \___/ . MM SPLINE: no convergence on required accuracy (adjust * * | EPS_SPLINE and rerun) * * O/| * * /| | * * / \ pair_potential.F:426 * ******************************************************************************* ===== Routine Calling Stack ===== 7 spline_nonbond_control 6 force_field_pack_splines 5 force_field_pack 4 force_field_control 3 fist_init 2 fist_create_force_env 1 CP2K ``` I suspect this is happening because I did not explicitly specify that each 5-atom unit is a single molecule, so CP2K is applying the Lennard-Jones potential between atoms that should be bonded. Since the atoms within each molecule are very close together, CP2K treats them as interacting via nonbonded forces, which leads to numerical instability in the Lennard-Jones calculations. **If my assumption is correc**, How can I properly define a molecule in CP2K using the 5 carbon atoms? How can I exclude Lennard-Jones interactions **within the same molecule**, while keeping them for interactions between different molecules? N.B: I understand that the carbon atoms are very close together, but this is a minimum working example meant to illustrate the issue. I cannot change the atomic positions, as the actual problem requires keeping them fixed. Also I want to ignore the bond vibrations, rotations, torsions etc. Any help or guidance would be greatly appreciated! </blockquote></div> -- You received this message because you are subscribed to a topic in the Google Groups "cp2k" group. To unsubscribe from this topic, visit <a href="https://groups.google.com/d/topic/cp2k/V5RlsZPw1Lk/unsubscribe" target="_blank">https://groups.google.com/d/topic/cp2k/V5RlsZPw1Lk/unsubscribe</a>. To unsubscribe from this group and all its topics, send an email to <a href="mailto:cp2k+unsubscribe@googlegroups.com" target="_blank">cp2k+unsubscribe@googlegroups.com</a>. To view this discussion visit <a href="https://groups.google.com/d/msgid/cp2k/c8965abb-ad8a-41c7-98b1-ca8674207b75n%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank">https://groups.google.com/d/msgid/cp2k/c8965abb-ad8a-41c7-98b1-ca8674207b75n%40googlegroups.com</a>. </blockquote></div> -- 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 <a href="mailto:cp2k+unsubscribe@googlegroups.com">cp2k+unsubscribe@googlegroups.com</a>. To view this discussion visit <a href="https://groups.google.com/d/msgid/cp2k/CAFgiMy-_FJd1Yuhg-LF%3DruX%2BRfQ-4zXpvQdZna0-yNYxpF-qsQ%40mail.gmail.com?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/CAFgiMy-_FJd1Yuhg-LF%3DruX%2BRfQ-4zXpvQdZna0-yNYxpF-qsQ%40mail.gmail.com</a>.