[CP2K-user] [CP2K:20357] Re: Help with Description header for RMSD COLVAR missing!!

[Marcella Iannuzzi]

Hi Edwin, 

The warning refers to the missing description of the CV in the output, but 
this does not affect the calculation. 
To calculate the RMSD only on a subset of atoms, please activate the 
corresponding key
SUBSET_TYPE LIST
Regards
Marcella

On Wednesday, June 19, 2024 at 7:18:59 PM UTC+2 helb... at gmail.com wrote:

> Dear All,
>
> I am trying to crate a Free Energy surface as in exercise 
> https://www.cp2k.org/exercises:2021_uzh_acpc2:ex03, 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 ../fm_216_2.xyz
> &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 ../fm_216_2.xyz
> &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.
>

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