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Re: [lammps-users] Fwd:

From: Giacomo Fiorin <giacomo.fiorin@...24...>
Date: Sat, 12 Aug 2017 14:07:04 -0400

Hello Ialtu, please ask a specific question after reading the documentation relevant to what you are trying to do.


On Sat, Aug 12, 2017 at 8:47 AM, laltu dass <tanni222byc@...24...> wrote:

---------- Forwarded message ----------
From: laltu dass <tanni222byc@...24...>
Date: Sat, Aug 12, 2017 at 4:59 PM
Subject: Re:
To: Axel Kohlmeyer <akohlmey@...24...>

thanks a lot sir,

now its running and i got some files created but unable to sort out which one is giving me the angle information?as it is written in the manual that orientationProj ,The returned value is the cosine of the angle of rotation q between the current and the reference positions. The range of values is [-1:1].

this are the output files created


fix        2 all colvars

fix 2 all colvars input out.colvars.state output out2

On Sat, Aug 12, 2017 at 4:26 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:

On Sat, Aug 12, 2017 at 2:31 AM, laltu dass <tanni222byc@...24...> wrote:
Respected sir,

i want to calculate Orientational ordering by calculating Legendre polynomial. i.e., P2(θ) )〈(3cos 2θ - 1)/2〉, in which θ is the angle between a direction vector and the surface normal

for that i am using lammps colvar

colvarsTrajFrequency 1
colvarsRestartFrequency 10
indexFile allindex.ndx

colvar {

    name one

    outputAppliedForce on

    width 0.5

  orientationProj {
        atoms {
            indexGroup cation
            centerReference yes
            rotateReference yes
            refPositionsGroup {
                indexGroup anion

harmonic {
    colvars        one
    centers        (1.0, 0.0, 0.0, 0.0)
    forceConstant  0.001

but getting error everytime colvars: Error: in parsing "centers"

​from the manual:

​enters ⟨Initial harmonic restraint centers⟩
Context: harmonic
Acceptable values: space-separated list of colvar values 




Dr. Axel Kohlmeyer  akohlmey@...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD