From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Aug 02 2021 - 09:51:37 CDT
There are multiple keywords to select atoms, one is atomNumbers followed by
numeric indices, or atomsFile as you have used. These two and other ones
live inside a block that is named like the group that is used by a variable
(e.g. for RMSD that group is called "atoms").
There are not a ton of examples in the Colvars doc. But selecting atoms is
a central topic and *there is actually one*:
https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html*sec:colvar_atom_groups_sel__;Iw!!DZ3fjg!s-QsiY4Gh_ZF8IaOcHWtxNM347secG374HFzVgavlTK0ETF7Sn4QbqMvy4A5dg-2TA$
There are also a couple more typos, which would give you additional errors
once you fix the syntax of the atom selection. You can easily fix them
yourself by giving a second read to what you put in.
Giacomo
On Mon, Aug 2, 2021 at 4:36 AM Vidhya Sankar <
vidhyasankar7928_at_remove_yahoo.com> wrote:
> Dear Namd users
> I am using rmsd as CV in namd
> for that i have input fie as follows
>
> colvar {
> name r1
>
> width 1
>
> lowerboundary 70
> upperboundary 145
>
> lowerwallconstant 10.0
> upperwallconstant 10.0
>
> # scriptedFunction source.tcl
>
> # extendedLagrangian on
> # extendedFluctuation 0.01
>
> rmsd {
> atoms { 1 2 3 4 5 }
> atomsFile 0.pdb
> atomsCol B
> atomsColValue 1.0
> # }
> refpositionsfile 1000.pdb
> refpositiosCol B
> refPositionsColvValue 1.0
> componentExp 1
> }
> }
>
> But When i run the simulation I got error as follows
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> *colvars: # scriptingAfterBiases = off [default] colvars:
> ----------------------------------------------------------------------
> colvars: Initializing a new collective variable. colvars: # name = "r1"
> colvars: Initializing a new "rmsd" component. colvars: # name = ""
> [default] colvars: # componentCoeff = 1 [default] colvars: #
> componentExp = 1 colvars: # period = 0 [default] colvars: #
> wrapAround = 0 [default] colvars: # forceNoPBC = off [default]
> colvars: # scalable = on [default] colvars: Initializing atom
> group "atoms". colvars: # name = "" [default] colvars: #
> centerReference = off [default] colvars: # rotateReference = off
> [default] colvars: # atomsOfGroup = "" [default] colvars: #
> indexGroup = "" [default] colvars: # psfSegID = [default]
> colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0
> , 0 , 0 ) [default] colvars: Error: no atoms defined for atom group
> "atoms". FATAL ERROR: Error in the collective variables module: exiting.
> ------------- Processor 0 Exiting: Called CmiAbort ------------ *
>
> *Reason: FATAL ERROR: Error in the collective variables module: exiting.*
>
>
> *It would be highly appreciable if any one point out and rectify the error
> for the past 10 days to me it was tedious to solve the error *
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> *With High regardsS.VIDHYA sankar*
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