<div dir="ltr">Dear Andreas, Ari and Marco Your suggestion is helpful. But i still i am missing one point. Suppose i am fixing for larger system (suppose 32 water molecules), then how can i fix the distance between oxygen and hydrogen of water. I mean do i need to define bond for each bonded atom pair separately for distance in COLVAR ? Is there some way to define molecule? For DFT calculation, i am just using atom ID (O or H) and its positions in random order. I hope for some suggestion. Thank you so much On Thursday, 13 November 2014 13:47:30 UTC+1, Andreas Funk wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">Dear Wei, The first thing I see in your input is that you specify one colvar in SUBSYS, but in MOTION you call two colvars. This cannot work. As it is only one bond you specify as colvar, you should work with one colvar in the CONSTRAINT section. Then you should keep it "fixed" like this in section MOTION: &CONSTRAINT &COLLECTIVE COLVAR 1 INTERMOLECULAR TARGET 2.399706 &RESTRAINT K 1.0 &END RESTRAINT &END COLLECTIVE &END CONSTRAINT Please keep in mind that the distance you want it to be fixed (TARGET) is in bohrs, not angstroms. You need to experiment a little with the force constant for the restraint. Check it in your runs if it is sufficient to keep the bond length fixed within your desired accuracy. In principle, it should do the job. I have used this kind of constraint successfully for both, geometry optimizations and MD. Best regards Andreas Am Donnerstag, 13. November 2014 12:31:24 UTC+1 schrieb Wei:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear Pankaj, Ari and Marco, I'd also like to fix a bond during a MD (DFT) run (not the absolute atomic positions). I tried to specify CP2K_INPUT / MOTION / CONSTRAINT / COLLECTIVE and CP2K_INPUT / FORCE_EVAL / SUBSYS / COLVAR by following an expample from regtest /Fist/regtest-12/water_3_dist_2.inp. However, the calculation always crashes with an error: * *** 12:16:30 ERRORL2 in topology_input:read_constraints_section processor *** *** 0 err=-300 condition FAILED at line 561 *** * ===== Routine Calling Stack ===== 3 topology_control 2 quickstep_create_force_env 1 CP2K CP2K| condition FAILED at line 561 CP2K| Abnormal program termination, stopped by process number 0 Could you please give me some hint on this issue? I put my input file below. Thanks in advance! Best Regards Wei input &FORCE_EVAL METHOD QUICKSTEP &DFT BASIS_SET_FILE_NAME ./GST.qbs POTENTIAL_FILE_NAME ./GTH_POTENTIALS &MGRID CUTOFF 300 &END MGRID &QS EPS_DEFAULT 1.0e-12 EXTRAPOLATION ASPC EXTRAPOLATION_ORDER 0 MAP_CONSISTENT &END QS &SCF EPS_SCF 1.0e-7 MAX_SCF 40 MAX_SCF_HIST 2 &OT ON MINIMIZER DIIS PRECONDITIONER FULL_KINETIC ENERGY_GAP 0.002 STEPSIZE 0.0875 &END OT &OUTER_SCF ON MAX_SCF 800 EPS_SCF 1.0e-7 &END OUTER_SCF SCF_GUESS RANDOM # SCF_GUESS HISTORY_RESTART &END SCF &XC &XC_FUNCTIONAL PBE &END XC_FUNCTIONAL &END XC &END DFT &SUBSYS &CELL ABC 18.62463 18.62463 18.62463 &END CELL &COORD Ge 10.0 10.0 10.0 bond Te 13.0 10.0 10.0 bond &END COORD &COLVAR &DISTANCE ATOMS 1 2 &END DISTANCE &END COLVAR &KIND Ge BASIS_SET DZVP-MOLOPT-SR-GTH-q4 POTENTIAL GTH-PBE-q4 &END KIND &KIND Te BASIS_SET DZVP-MOLOPT-SR-GTH-q6 POTENTIAL GTH-PBE-q6 &END KIND &END SUBSYS &END FORCE_EVAL &GLOBAL PREFERRED_FFT_LIBRARY FFTW PRINT_LEVEL LOW PROJECT GeTe.md RUN_TYPE MD &END GLOBAL &MOTION &MD ENSEMBLE LANGEVIN STEPS 20 TEMPERATURE 1100 TIMESTEP 2.0 &LANGEVIN GAMMA 4.0E-3 NOISY_GAMMA 3.5E-5 &END LANGEVIN &END MD &CONSTRAINT &COLLECTIVE MOLNAME bond COLVAR 1 &END COLLECTIVE &COLLECTIVE MOLNAME bond COLVAR 2 &END COLLECTIVE &END CONSTRAINT &END MOTION<div dir="ltr"><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"> </div></blockquote></div></blockquote></div></div></blockquote></div></blockquote></div>