From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed May 18 2016 - 08:23:14 CDT
Hello Sourav you probably want distancexy instead of distancedir?
Giacomo
On May 18, 2016 8:53 AM, "Sourav Ray" <souravray90_at_gmail.com> wrote:
> Hello
>
> I am trying to vary the distance between two carbon nanotubes along
> x-axis. Additionally, I would like to restrict any rotation, whatsoever,
> and translation along y and z axes. I am using "Distancedir" to restrict
> translation for both the nano-tubes along y and z axes and "orient" to
> restrict rotation with "harmonic" constraint. However, I am not getting the
> desired effect. Please find the colvars script below:
>
>
> colvarsTrajFrequency 10000
> colvarsRestartFrequency 10000
>
>
> colvar {
>
> name cntdis
> width 0.1
> lowerboundary 12.0
> upperboundary 20.0
> lowerwallconstant 100.0
> upperwallconstant 100.0
>
>
> distance {
> group1 {
> atomnumbersrange { 1-364 }
> }
>
> group2 {
> atomnumbersrange { 365-728 }
> }
>
> }
> }
>
> colvar {
> name orient
>
> width 0.1 # distance between quaternions is from 0 to pi/2, so small
> fluctuations are significant
>
> orientation {
> atoms {
> atomNumbersrange { 1-728 }
> enableForces off
> }
> refPositionsFile ../ref.pdb # Fetch initial positions from this
> file
> }
> }
>
>
> colvar {
>
> name ztrans1
> width 0.1
>
> distancedir {
> group1 {
> atomnumbersrange { 1-364 }
> }
>
> group2 {
> dummyatom (-6.5,0,0)
> }
> }
> }
>
> colvar {
>
> name ztrans2
> width 0.1
>
> distancedir {
> group1 {
> atomnumbersrange { 365-728 }
> }
>
> group2 {
> dummyatom (6.5,0,0)
> }
> }
>
>
> harmonic {
> colvars orient ztrans1 ztrans2
> centers (1,0,0,0) (1,0,0) (1,0,0)
> forceconstant 10.0
> }
> metadynamics {
> colvars cntdis
> hillWidth 2
> hillWeight 0.5
> newHillFrequency 100
> }
>
>
> Please let me know if someone has any insight regarding the same.
>
> Regards
> Sourav
>
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