<div dir="ltr">Dear Marcella,<div><br></div><div>Thanks you for your reply. I have understand now.</div><div><br></div><div><div> <b><i> &COLVAR</i></b></div><div><b><i> &COORDINATION</i></b></div><div><b><i> ATOMS_FROM 1</i></b></div><div><b><i> ATOMS_TO 2 3</i></b></div><div><b><i> R_0 2.3</i></b></div><div><b><i> &END COORDINATION</i></b></div></div><div><br></div><div> I can understand the section above that the "number" of atoms of type 2 <b><i>and type 3</i></b> that are within a given radius (2.3) from atoms of type 1, in average, right??</div><div><br></div><div> Furthermore, the output results included a file "***-COLVAR.metadynLog",</div><div><div> <i> 0.00000000 1.61674 0.00000 0.00000 0.00000 0.00000</i></div><div><i> 0.50000000 1.61884 0.00000 0.00000 0.00000 0.00000</i></div><div><i> 1.00000000 1.61648 0.00000 0.00000 0.00100 0.00000</i></div><div><i> 1.50000000 1.60987 -0.01564 0.00000 0.00095 0.00000</i></div><div><i> 2.00000000 1.59765 -0.03022 0.00000 0.00164 0.00000</i></div><div><i> 2.50000000 1.57905 -0.04642 0.00000 0.00082 0.00000</i></div><div><i> 3.00000000 1.55352 -0.01078 0.00000 0.00109 0.00000</i></div><div><i> 3.50000000 1.52892 -0.02935 0.00000 0.00047 0.00000</i></div><div><i> 4.00000000 1.50514 -0.00649 0.00000 0.00105 0.00000</i></div><div><i> 4.50000000 1.48856 -0.03022 0.00000 0.00071 0.00000</i></div><div><i> 5.00000000 1.47702 -0.02630 0.00000 0.00137 0.00000</i></div><div><i> 0.00000000 1.61674 0.00000 0.00000 0.00000 0.00000</i></div><div><i> 0.50000000 1.61884 0.00000 0.00000 0.00000 0.00000</i></div><div><i> 1.00000000 1.61648 0.00000 0.00000 0.00100 0.00000</i></div><div><i> 1.50000000 1.60987 -0.01564 0.00000 0.00095 0.00000</i></div><div><i> 2.00000000 1.59765 -0.03022 0.00000 0.00164 0.00000</i></div><div><i> 2.50000000 1.57905 -0.04642 0.00000 0.00082 0.00000</i></div><div><i> 3.00000000 1.55352 -0.01078 0.00000 0.00109 0.00000</i></div><div><i> 3.50000000 1.52892 -0.02935 0.00000 0.00047 0.00000</i></div><div><i> 4.00000000 1.50514 -0.00649 0.00000 0.00105 0.00000</i></div><div><i> 4.50000000 1.48856 -0.03022 0.00000 0.00071 0.00000</i></div><div><i> 5.00000000 1.47702 -0.02630 0.00000 0.00137 0.00000</i></div><div><i>......</i></div><div><br></div><div><br></div><div>and a file "***-HILLS.metadynLog"</div><div><br></div><div><div> <i> 1.0 1.61648 0.02000 0.00100</i></div><div><i> 2.0 1.59765 0.02000 0.00100</i></div><div><i> 3.0 1.55352 0.02000 0.00100</i></div><div><i> 4.0 1.50514 0.02000 0.00100</i></div><div><i> 5.0 1.47702 0.02000 0.00100</i></div><div><i> 1.0 1.61648 0.02000 0.00100</i></div><div><i> 2.0 1.59765 0.02000 0.00100</i></div><div><i> 3.0 1.55352 0.02000 0.00100</i></div><div><i> 4.0 1.50514 0.02000 0.00100</i></div><div><i> 5.0 1.47702 0.02000 0.00100</i></div><div><i> 6.0 1.47374 0.02000 0.00100</i></div><div><i> 7.0 1.49936 0.02000 0.00100</i></div><div><i> 8.0 1.57313 0.02000 0.00100</i></div><div><i> 9.0 1.64781 0.02000 0.00100</i></div><div><i> 10.0 1.69384 0.02000 0.00100</i></div><div><i> 11.0 1.68170 0.02000 0.00100</i></div><div><i> 12.0 1.61092 0.02000 0.00100</i></div><div><i> 13.0 1.51437 0.02000 0.00100</i></div><div><i> 14.0 1.44559 0.02000 0.00100</i></div><div><i> 15.0 1.39573 0.02000 0.00100</i></div><div><i> 16.0 1.40930 0.02000 0.00100</i></div><div><i> 17.0 1.48566 0.02000 0.00100</i></div><div><i> 18.0 1.58976 0.02000 0.00100</i></div><div><i> 19.0 1.68096 0.02000 0.00100</i></div><div><i> 20.0 1.72275 0.02000 0.00100</i></div><div><i> 21.0 1.70510 0.02000 0.00100</i></div><div><i> 22.0 1.62193 0.02000 0.00100</i></div><div><i> 23.0 1.50355 0.02000 0.00100</i></div><div><i> 24.0 1.40440 0.02000 0.00100</i></div></div><div><i>.......</i></div><div><br></div><div>But I don't understand what does every column stand for? Would you help me? How can I get the figure of FES VS CV? </div><div><br></div><div>Thanks.</div><div><br></div><div>Ning</div><div><br></div><br>在 2015年9月8日星期二 UTC+8下午3:22:25，Marcella Iannuzzi写道：<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear .....<div><br></div><div>Every COLVAR has different keywords depending on its functional definition.</div><div>In the specific case, the coordination is defined as the "number" of atoms of type 2 that are within a given radius from atoms of type 1, in average.</div><div>Regards</div><div>Marcella<br><br>On Monday, September 7, 2015 at 1:02:24 PM UTC+2, <a>ning....@gmail.com</a> wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">I am newer for the cp2k. I am studying the metadynamics method. I noted that colvars section in the input files includes the keywords atoms_from and atoms_to. I don't understand what does it mean? what does the R_0 stand for?? For example, see the bold text<div><br></div><div><div>&FORCE_EVAL</div><div> METHOD Quickstep</div><div> &DFT</div><div> BASIS_SET_FILE_NAME BASIS_SET</div><div> POTENTIAL_FILE_NAME POTENTIAL</div><div> &MGRID</div><div> CUTOFF 200</div><div> &END MGRID</div><div> &QS</div><div> &END QS</div><div> &SCF</div><div> SCF_GUESS ATOMIC</div><div> &END SCF</div><div> &XC</div><div> &XC_FUNCTIONAL Pade</div><div> &END XC_FUNCTIONAL</div><div> &END XC</div><div> &END DFT</div><div> &SUBSYS</div><div> &CELL</div><div> ABC 5.0 5.0 5.0</div><div> &END CELL</div><div> &COORD</div><div> O 0.000000 0.000000 -0.065587</div><div> H 0.000000 -0.757136 0.520545</div><div> H 0.000000 0.757136 0.520545</div><div> &END COORD</div><div> &KIND H</div><div> BASIS_SET DZVP-GTH-PADE</div><div> POTENTIAL GTH-PADE-q1</div><div> &END KIND</div><div> &KIND O</div><div> BASIS_SET DZVP-GTH-PADE</div><div> POTENTIAL GTH-PADE-q6</div><div> &END KIND</div><div> <b><i> &COLVAR</i></b></div><div><b><i> &COORDINATION</i></b></div><div><b><i> ATOMS_FROM 1</i></b></div><div><b><i> ATOMS_TO 2 3</i></b></div><div><b><i> R_0 2.3</i></b></div><div><b><i> &END COORDINATION</i></b></div><div> &END COLVAR</div><div> &END SUBSYS</div><div>&END FORCE_EVAL</div><div>&GLOBAL</div><div> PROJECT H2O-meta_coord</div><div> RUN_TYPE MD</div><div> PRINT_LEVEL LOW</div><div>&END GLOBAL</div><div>&MOTION</div><div> &MD</div><div> ENSEMBLE NVT</div><div> STEPS 10000</div><div> TIMESTEP 0.5</div><div> TEMPERATURE 300.0</div><div> &THERMOSTAT</div><div> &NOSE</div><div> LENGTH 3</div><div> YOSHIDA 3</div><div> TIMECON 100.0</div><div> MTS 2</div><div> &END NOSE</div><div> &END</div><div> &END MD</div><div> &FREE_ENERGY</div><div> &METADYN</div><div> DO_HILLS</div><div> NT_HILLS 2</div><div> WW 1.0e-3</div><div> &METAVAR</div><div> SCALE 0.02</div><div> COLVAR 1</div><div> &END METAVAR</div><div> &PRINT</div><div> &COLVAR</div><div> COMMON_ITERATION_LEVELS 3</div><div> &END</div><div> &HILLS</div><div> COMMON_ITERATION_LEVELS 3</div><div> &END</div><div> &END</div><div> &END METADYN</div><div> &END</div><div>&END MOTION</div></div><div><br></div><div>Any provides are welcome.</div><div><br></div></div></blockquote></div></div></blockquote></div></div>