Hi Edwin, <div> </div><div>The warning refers to the missing description of the CV in the output, but this does not affect the calculation. </div><div>To calculate the RMSD only on a subset of atoms, please activate the corresponding key</div><div>SUBSET_TYPE LIST</div><div>Regards</div><div>Marcella </div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, June 19, 2024 at 7:18:59 PM UTC+2 helb...@gmail.com wrote: </div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Dear All, I am trying to crate a Free Energy surface as in exercise <a href="https://www.cp2k.org/exercises:2021_uzh_acpc2:ex03" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://www.cp2k.org/exercises:2021_uzh_acpc2:ex03&source=gmail&ust=1718955522588000&usg=AOvVaw2A8_fMUBLTf2SbH682vZWN">https://www.cp2k.org/exercises:2021_uzh_acpc2:ex03</a>, but I want some of the collective variables to be the RMSD to a reference structure. I am defining COLVAR in the following way: &COLVAR &DISTANCE ! First helix &POINT TYPE GEO_CENTER ! N CA C O ATOMS 67 69 75 76 &END ! Second helix &POINT TYPE GEO_CENTER ! N CA C O ATOMS 250 252 258 259 &END POINTS 1 2 &END &END COLVAR &COLVAR &RMSD ALIGN_FRAMES .TRUE. ATOMS 7 9 15 16 17 19 25 26 27 29 35 36 37 39 45 46 47 49 55 56 57 59 65 66 67 69 75 76 77 79 85 86 87 89 95 96 97 99 105 106 107 109 115 116 117 119 125 126 127 129 135 136 137 139 145 146 &FRAME COORD_FILE_NAME ../<a href="http://fm_216_2.xyz" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://fm_216_2.xyz&source=gmail&ust=1718955522588000&usg=AOvVaw3AXXoxk_nS8Q7_QmczufY6">fm_216_2.xyz</a> &END &END &END COLVAR &COLVAR &RMSD ALIGN_FRAMES .TRUE. ATOMS 190 192 198 199 200 202 208 209 210 212 218 219 220 222 228 229 230 232 238 239 240 242 248 249 250 252 258 259 260 262 268 269 270 272 278 279 280 282 288 289 290 292 298 299 300 302 308 309 310 312 308 309 310 312 318 319 320 322 328 329 &FRAME COORD_FILE_NAME ../<a href="http://fm_216_2.xyz" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://fm_216_2.xyz&source=gmail&ust=1718955522588000&usg=AOvVaw3AXXoxk_nS8Q7_QmczufY6">fm_216_2.xyz</a> &END &END &END COLVAR &END SUBSYS However, even though the simulation is running correctly, I am getting the following warning in the output file ---------------------------------------------------------------------- ---------------------------------------------------------------------- COLVARS| COLVAR INPUT INDEX: 2 *** WARNING in colvar_methods.F:1271 :: Description header for RMSD *** *** COLVAR missing!! *** ---------------------------------------------------------------------- ---------------------------------------------------------------------- COLVARS| COLVAR INPUT INDEX: 3 *** WARNING in colvar_methods.F:1271 :: Description header for RMSD *** *** COLVAR missing!! *** ---------------------------------------------------------------------- and the values corresponding to the RMSD CVs in the *.metadynLog file don't make sense. Thanks in advance. Kind regards, Edwin. </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 on the web visit <a href="https://groups.google.com/d/msgid/cp2k/9e1822e6-3cd6-43b0-a5fe-af2bee476c3cn%40googlegroups.com?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/9e1822e6-3cd6-43b0-a5fe-af2bee476c3cn%40googlegroups.com</a>.