[CP2K-user] [CP2K:20401] Re: Help with Description header for RMSD COLVAR missing!!

[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... 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 <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 <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.
> 
> -- 
> 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 cp2k+unsubscribe at googlegroups.com 
> <mailto:cp2k+unsubscribe at googlegroups.com>.
> To view this discussion on the web visit https://groups.google.com/d/ 
> msgid/cp2k/9e1822e6-3cd6-43b0-a5fe-af2bee476c3cn%40googlegroups.com 
> <https://groups.google.com/d/msgid/cp2k/9e1822e6-3cd6-43b0-a5fe- 
> af2bee476c3cn%40googlegroups.com?utm_medium=email&utm_source=footer>.

-- 
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 cp2k+unsubscribe at googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/23c71af0-abed-4193-8a52-16e4e109320e%40gmail.com.