Hi <span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Arial;">Jianfeng Jia</span><div><font color="#000000" face="Arial"><span style="caret-color: rgb(0, 0, 0);"><br /></span></font></div><div><font color="#000000" face="Arial"><span style="caret-color: rgb(0, 0, 0);">The CV is never negative, as reported in the COLVAR output. </span></font></div><div><font color="#000000" face="Arial">In the first part of the simulation, it is almost zero, and the metadynamics hills have a width of 0.2, meaning that they extend to negative values.</font></div><div><font color="#000000" face="Arial"><br /></font></div><div><font color="#000000" face="Arial">Regards</font></div><div><font color="#000000" face="Arial">Marcella</font></div><div><br /></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Sunday, May 26, 2024 at 9:38:31 AM UTC+2 jjf_sxtu@yahoo.com.cn wrote:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial"><div style="margin:0">Dear CP2K experts,</div><div style="margin:0"> I want ot use cp2k to do a metadynamics calculation to get the free energy change for a reaction. I use the coordination number of a O atom to all H atoms as CV (this O-H bond will be formed in the reaction) to do the metadynamic calculation. </div><div style="margin:0">the CV was defined as:</div><div style="margin:0"><div style="margin:0"> &COLVAR</div><div style="margin:0"> &COORDINATION</div><div style="margin:0"> ATOMS_FROM 61</div><div style="margin:0"> KINDS_TO H</div><div style="margin:0"> R0 [angstrom] 0.93</div><div style="margin:0"> NN 8</div><div style="margin:0"> ND 14</div><div style="margin:0"> &END COORDINATION</div><div style="margin:0"> &END COLVAR</div><div style="margin:0"><br></div><div style="margin:0">For metadynamics:</div><div style="margin:0"><br></div><div style="margin:0"><div style="margin:0"> &METADYN</div><div style="margin:0"> DO_HILLS</div><div style="margin:0"> NT_HILLS 80</div><div style="margin:0"> WW 3.0e-3</div><div style="margin:0"><br></div><div style="margin:0"> &METAVAR</div><div style="margin:0"> SCALE 0.2</div><div style="margin:0"> COLVAR 1</div><div style="margin:0"> &END METAVAR</div><div style="margin:0"><br></div><div style="margin:0">When the job was ended, I get the fes.dat file by using the command: graph.psmp -cp2k -ndim 1 -ndw 1 -file aimd-1.restart. This file looks like:</div><div style="margin:0"><div style="margin:0"> -0.5800822901 -0.0005584043</div><div style="margin:0"> -0.5464051991 -0.0009289081</div><div style="margin:0"> -0.<a href="tel:(512)%20728-1080" value="+15127281080" target="_blank" rel="nofollow">5127281080</a> -0.0015031205</div><div style="margin:0"> -0.4790510169 -0.0023662732</div><div style="margin:0"> -0.<a href="tel:(445)%20373-9259" value="+14453739259" target="_blank" rel="nofollow">4453739259</a> -0.0036245468</div><div style="margin:0"> -0.4116968348 -0.0054030940</div><div style="margin:0"> -0.3780197438 -0.0078403220</div><div style="margin:0"> -0.3443426527 -0.0110778295</div><div style="margin:0"> -0.<a href="tel:(310)%20665-5617" value="+13106655617" target="_blank" rel="nofollow">3106655617</a> -0.0152462075</div><div style="margin:0">........</div><div style="margin:0"><br></div><div style="margin:0">My question is why the CV vaules in the first column can be negative? My CV is the coordination number. I think it should be positive anyway. The whole input file and corresponding xyz file and some output file were attached in this letter. Please help me.</div><div style="margin:0"><br></div><div style="margin:0">Jianfeng Jia</div><div style="margin:0"><br></div></div><div style="margin:0"><br></div><div style="margin:0"><br></div></div></div></div></blockquote></div>
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