orient colvars

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#1

Hi All,

I want to fix the orientation of a molecules (with atom number 1 to 100) using colvars.My question is regarding the referencing atoms. In NAMD we can reference a pdb file. How is this done in LAMMPS ? The colvar manual used NAMD syntax.

colvar {
name Orient

orientation {
atoms {
atomnumbersRange {1-100}
}
refPositionsGroup {
atomnumbersRange {1-100}
}
#ref {
#atomnumbersRange {1-100}
}
}
}

harmonic {
colvars Orient
centers (1.0, 0.0, 0.0, 0.0)
forceConstant 10.0
}

The above syntax generating the error: Error: must define a set of reference coordinates. The problem is in defining the reference structure. What is the right syntax.

Thank you.

#2

Hi All,

I want to fix the orientation of a molecules (with atom number 1 to 100)
using colvars.My question is regarding the referencing atoms. In NAMD we can
reference a pdb file. How is this done in LAMMPS ? The colvar manual used

this functionality is currently missing in the LAMMPS interface to colvars.
LAMMPS doesn't have the PDB file parser that is used in NAMD.
not sure what would be the LAMMPS way of doing things like this. need
to think about it.

axel.

#3

Hello Sridhar, please use an xyz file in lammps.

Giacomo