rmsd colvars atom definition

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Apr 10 2020 - 01:44:55 CDT

Hello
I am looking for advice on defining <atomNameResidueRange> for rmsd
colvars. As shown below, I could define one atom only. To this concern, I
tried also <atomNameResidueRange P N1 2820-2821>
which was not accepted.

Moreover, is it possible to define residue names in place of atom names?

> colvar {
> name colvar1 # needed to identify the variable
> lowerBoundary -2.0
> upperBoundary 2.0 ;# force will kick in when rmsd exceeds 2 A
>
>
> lowerWall -1.5 ;# a lttle higher than lowerBoundary
> upperWall 1.5 ;# a little lower than upperBoundary
>
> lowerWallConstant 100.0 ;# force constant in kcal/mol
> upperWallConstant 100.0
> outputTotalForce yes # reports also colvar system force
>
>
> rmsd {
> atoms {
> # add all the C-alphas within residues 2820-2821 of segment AN7
> psfSegID AN7
> atomNameResidueRange N1 2820-2821
> }
> # refPositionsFile sphere20_CEA_box_ion.pdb
> }
> ref PositionsCol X, Y, Z
> }
>
> colvar {
> name colvar2 # needed to identify the variable
> lowerBoundary -2.0
> upperBoundary 2.0 ;# force will kick in when rmsd exceeds 2 A
>
> lowerWall -1.5 ;# a lttle higher than lowerBoundary
> upperWall 1.5 ;# a little lower than upperBoundary
>
> lowerWallConstant 100.0 ;# force constant in kcal/mol
> upperWallConstant 100.0
>
> outputTotalForce yes # reports also colvar system force
>
>
> rmsd {
> atoms {
> # add all the C-alphas within residues 2869-2875 of segment AN8
> psfSegID AN8
> atomNameResidueRange N1 2869-2875
> }
> refPositionsFile sphere20_CEA_box_ion.pdb
> }
> # refPositionsCol X, Y, Z
> }
>
> harmonic {
>
> name AN7_harmonic
>
> colvars { colvar1 }
>
> centers 0.0
>
> forceConstant 10.0
> }
>
> harmonic {
>
> name AN8_harmonic
>
> colvars { colvar2 }
>
> centers 0.0
>
> forceConstant 10.0
> }
>

Thanks
francesco pietra

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