Help with Description header for RMSD COLVAR missing!!

[Edwin Helbert Aponte Angarita]

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.

[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

[Edwin Helbert Aponte Angarita]

Sorry for the late reply. Thank you Marcella for answering my question.
I am running again the calculation, this time with SUBSET_TYPE LIST
inside the RMSD subsection.

Regards,
Edwin.

On 6/20/24 8:58 AM, Marcella Iannuzzi wrote:
> 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...@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 <https://
> www.cp2k.org/exercises:2021_uzh_acpc2:ex03>, but I want some of

> COORD_FILE_NAME ../fm_216_2.xyz <http://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 <http://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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