<div dir="ltr">Dear all,<div>I am studying cp2k, and I want to use umbrella integration to calculate the PMF of NaCl. Here follows the example of the input files of NaCl solution, and the distance of Na-Cl is 2.5 A. Some part of the output file was followed. I am wondering what meaning of (<font color="#ff0000">eval_cov_matrix 82 84 4.8791450923533191 1.2895562591097587E-004</font>) and how could them be used to calculate the free energy?</div><div><br></div><div>Many thanks for your help.</div><div>Merry Chrismas!</div><div><br></div><div>Wei</div><div><br></div><div><div><div>#</div><div># NaCl in water</div><div>#</div><div>&FORCE_EVAL</div><div> METHOD FIST</div><div> &MM</div><div> &FORCEFIELD</div><div> &SPLINE</div><div> EMAX_SPLINE 300000.0</div><div> &END</div><div> &BEND</div><div> ATOMS H O H</div><div> KIND HARMONIC</div><div> K [rad^-2kcalmol] 110.0</div><div> THETA0 [deg] 104.52</div><div> &END BEND</div><div> &BOND</div><div> ATOMS O H</div><div> KIND HARMONIC</div><div> K [angstrom^-2kcalmol] 900.0 </div><div> R0 [angstrom] 0.9572</div><div> &END BOND</div><div> &CHARGE</div><div> ATOM Na</div><div> CHARGE 1.0</div><div> &END CHARGE</div><div> &CHARGE</div><div> ATOM Cl</div><div> CHARGE -1.0</div><div> &END CHARGE</div><div> &CHARGE</div><div> ATOM O</div><div> CHARGE -0.834</div><div> &END CHARGE</div><div> &CHARGE</div><div> ATOM H</div><div> CHARGE 0.417</div><div> &END CHARGE</div><div> &NONBONDED</div><div> &LENNARD-JONES</div><div> atoms O O</div><div> EPSILON [kcalmol] 0.152073</div><div> SIGMA [angstrom] 3.1507</div><div> RCUT [angstrom] 11.4</div><div> &END LENNARD-JONES</div><div> &LENNARD-JONES</div><div> atoms O H</div><div> EPSILON [kcalmol] 0.0836</div><div> SIGMA [angstrom] 1.775</div><div> RCUT [angstrom] 11.4</div><div> &END LENNARD-JONES</div><div> &LENNARD-JONES</div><div> atoms H H</div><div> EPSILON [kcalmol] 0.04598</div><div> SIGMA [angstrom] 0.400</div><div> RCUT [angstrom] 11.4</div><div> &END LENNARD-JONES</div><div> &LENNARD-JONES</div><div> atoms Na Na</div><div> EPSILON [kcalmol] 0.0469</div><div> SIGMA [angstrom] 2.7275</div><div> RCUT [angstrom] 11.4</div><div> &END LENNARD-JONES</div><div> &LENNARD-JONES</div><div> atoms Na O</div><div> EPSILON [kcalmol] .08445</div><div> SIGMA [angstrom] 2.93</div><div> RCUT [angstrom] 11.4</div><div> &END LENNARD-JONES</div><div> &LENNARD-JONES</div><div> atoms Na H</div><div> EPSILON [kcalmol] .0464</div><div> SIGMA [angstrom] 1.5637</div><div> RCUT [angstrom] 11.4</div><div> &END LENNARD-JONES</div><div> &LENNARD-JONES</div><div> atoms Na Cl</div><div> EPSILON [kcalmol] .0838</div><div> SIGMA [angstrom] 3.63</div><div> RCUT [angstrom] 11.4</div><div> &END LENNARD-JONES</div><div> &LENNARD-JONES</div><div> atoms Cl Cl</div><div> EPSILON [kcalmol] 0.150</div><div> SIGMA [angstrom] 4.54</div><div> RCUT [angstrom] 11.4</div><div> &END LENNARD-JONES</div><div> &LENNARD-JONES</div><div> atoms Cl O</div><div> EPSILON [kcalmol] .151</div><div> SIGMA [angstrom] 3.84</div><div> RCUT [angstrom] 11.4</div><div> &END LENNARD-JONES</div><div> &LENNARD-JONES</div><div> atoms Cl H</div><div> EPSILON [kcalmol] .083</div><div> SIGMA [angstrom] 2.47</div><div> RCUT [angstrom] 11.4</div><div> &END LENNARD-JONES</div><div> &END NONBONDED</div><div> &END FORCEFIELD</div><div> &POISSON</div><div> &EWALD</div><div> EWALD_TYPE spme</div><div> ALPHA .3</div><div> GMAX 12</div><div> O_SPLINE 6</div><div> &END EWALD</div><div> &END POISSON</div><div> &END MM</div><div> &SUBSYS</div><div> &CELL</div><div> ABC 12.4138 12.4138 12.4138</div><div> &END CELL</div><div> &COORD</div><div>@INCLUDE 'coord-2.5'</div><div> &END COORD</div><div> &COLVAR</div><div> &DISTANCE</div><div> ATOMS 190 191</div><div> &END DISTANCE</div><div> !&PRINT</div><div> !&PROGRAM_RUN_INFO ON</div><div> ! &EACH</div><div> ! MD 1</div><div> ! &END EACH</div><div> !&END PROGRAM_RUN_INFO</div><div> !&END PRINT</div><div> &END COLVAR</div><div> &TOPOLOGY</div><div> CONNECTIVITY GENERATE</div><div> &GENERATE</div><div> BONDLENGTH_MAX 7</div><div> &END</div><div> &END</div><div> &END SUBSYS</div><div>&END FORCE_EVAL</div><div><br></div><div>&MOTION</div><div> &CONSTRAINT</div><div> &COLLECTIVE</div><div> COLVAR 1</div><div> INTERMOLECULAR</div><div> TARGET [angstrom] 2.5</div><div> &RESTRAINT</div><div> K [kcalmol] 200</div><div> &END RESTRAINT</div><div> &END COLLECTIVE</div><div> !&LAGRANGE_MULTIPLIERS</div><div> !COMMON_ITERATION_LEVELS 3</div><div> !&END</div><div> &END CONSTRAINT</div><div> &MD</div><div> ENSEMBLE NVT</div><div> TIMESTEP 0.5</div><div> STEPS 2000</div><div> TEMPERATURE 350</div><div> &THERMOSTAT</div><div> REGION GLOBAL </div><div> &NOSE</div><div> LENGTH 3</div><div> YOSHIDA 3</div><div> TIMECON 1000</div><div> MTS 2</div><div> &END NOSE</div><div> &END</div><div> &PRINT </div><div> &ENERGY</div><div> &EACH</div><div> MD 1</div><div> &END</div><div> &END ENERGY</div><div> !&PROGRAM_RUN_INFO</div><div> ! &EACH</div><div> ! MD 1</div><div> !&END</div><div> !&END PROGRAM_RUN_INFO</div><div> &END PRINT</div><div> &END MD</div><div> &PRINT </div><div> &TRAJECTORY</div><div> &EACH</div><div> MD 1</div><div> &END</div><div> &END</div><div> &VELOCITIES OFF</div><div> &END VELOCITIES</div><div> &FORCES OFF</div><div> &END FORCES</div><div> &RESTART_HISTORY OFF</div><div> &END RESTART_HISTORY </div><div> &RESTART OFF</div><div> &END RESTART</div><div> &END PRINT</div><div> &GEO_OPT</div><div> OPTIMIZER LBFGS</div><div> &END</div><div><br></div><div>&FREE_ENERGY</div><div> METHOD UI</div><div> &UMBRELLA_INTEGRATION</div><div> &CONVERGENCE_CONTROL</div><div> EPS_CONV 0.5</div><div> COARSE_GRAINED_WIDTH 3</div><div> MAX_COARSE_GRAINED_WIDTH 3</div><div> COARSE_GRAINED_POINTS 2</div><div> &END CONVERGENCE_CONTROL</div><div> &UVAR</div><div> COLVAR 1</div><div> &END UVAR</div><div> &END UMBRELLA_INTEGRATION</div><div> </div><div> &FREE_ENERGY_INFO</div><div> COMMON_ITERATION_LEVELS 1</div><div> &EACH </div><div> MD 1</div><div> &END EACH</div><div> &END FREE_ENERGY_INFO</div><div> &END</div><div>&END MOTION</div><div>&GLOBAL</div><div> PROJECT NACL-CONSTRAINED-2.5-3</div><div> RUN_TYPE MD</div><div> IOLEVEL LOW</div><div> &PRINT</div><div> PHYSCON</div><div> &END PRINT</div><div>&END GLOBAL</div></div><div><br></div><div><b><font color="#ff0000">output:</font></b></div><div><br></div><div><div> ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.): -1.140112705278208</div><div><br></div><div> COLVAR:: 4.8903632470564613 </div><div> 82 82</div><div><br></div><div> *******************************************************************************</div><div> ENSEMBLE TYPE = NVT</div><div> STEP NUMBER = 82</div><div> TIME [fs] = 41.000000</div><div> CONSERVED QUANTITY [hartree] = -0.846052947201E+00</div><div><br></div><div> INSTANTANEOUS AVERAGES</div><div> CPU TIME [s] = 0.01 0.01</div><div> ENERGY DRIFT PER ATOM [K] = 0.373834318693E+00 0.118177365928E-01</div><div> POTENTIAL ENERGY[hartree] = -0.114011270528E+01 -0.113335123442E+01</div><div> KINETIC ENERGY [hartree] = 0.292558333950E+00 0.286028884488E+00</div><div> TEMPERATURE [K] = 324.149 316.915</div><div> *******************************************************************************</div><div><br></div><div><br></div><div> ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.): -1.145923868073005</div><div><br></div><div> COLVAR:: 4.8794156731299481 </div><div> 83 83</div><div><br></div><div> *******************************************************************************</div><div> ENSEMBLE TYPE = NVT</div><div> STEP NUMBER = 83</div><div> TIME [fs] = 41.500000</div><div> CONSERVED QUANTITY [hartree] = -0.846293102603E+00</div><div><br></div><div> INSTANTANEOUS AVERAGES</div><div> CPU TIME [s] = 0.01 0.01</div><div> ENERGY DRIFT PER ATOM [K] = -0.232075005042E-01 0.113957457844E-01</div><div> POTENTIAL ENERGY[hartree] = -0.114592386807E+01 -0.113350271193E+01</div><div> KINETIC ENERGY [hartree] = 0.298118106873E+00 0.286174537770E+00</div><div> TEMPERATURE [K] = 330.309 317.076</div><div> *******************************************************************************</div><div><br></div><div><br></div><div> ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.): -1.151438173429435</div><div><br></div><div> COLVAR:: 4.8676563568735487 </div><div> 84 84</div><div> *******************************************************************************</div><div> FREE ENERGY CALCULATION</div><div><br></div><div> 84 3</div><div> 82 84</div><div> eval_cov_matrix 82 84 4.8791450923533191 1.2895562591097587E-004</div><div> 79 81</div><div> eval_cov_matrix 79 81 4.9088196261817298 6.8493458343255043E-005</div><div> 76 78</div><div> eval_cov_matrix 76 78 4.9276165349320822 1.7493356395448245E-005</div><div> 73 75</div><div> eval_cov_matrix 73 75 4.9331984582015895 4.2806313160781428E-007</div><div> 70 72</div><div> eval_cov_matrix 70 72 4.9248292229843216 2.5841844411900183E-005</div><div> 67 69</div><div> eval_cov_matrix 67 69 4.9034737225850238 8.2163081351893652E-005</div><div> 64 66</div><div> eval_cov_matrix 64 66 4.8717144712694900 1.4267166679360344E-004</div><div> 61 63</div><div> eval_cov_matrix 61 63 4.8334807396779205 1.7780849109527708E-004</div><div> 58 60</div><div> eval_cov_matrix 58 60 4.7936121609791531 1.6946047939825348E-004</div><div> 55 57</div><div> eval_cov_matrix 55 57 4.7572917091301408 1.2068974226764340E-004</div></div><div><br></div><div><br></div></div></div>