Restrict drift of Graphene sheet in X-Y plane using Colvars

From: ANIRBAN MANDAL (anirban.mandal_at_msc2015.iitgn.ac.in)
Date: Mon Mar 26 2018 - 05:04:55 CDT

Respected Sir/Madam,

I have set up a simulation for 1 nanosecond where my aim is to pull down a
Graphene sheet at the top of a water box with respect to another graphene
sheet containing a pore at the bottom using *NAMD Colvars Module*. I have
fixed two atoms of the bottom graphene sheet in order to ensure that the
sheet is fixed. After One nanosecond simulation, I found some kind of drift
of the top graphene sheet in the x-y plane. How can it be restricted to
come down vertically with any horizontal movement?

Colvars File attached below:

*Colvarstrajfrequency 1000Colvarsrestartfrequency 500colvar { name
dist distanceZ { main { atomNumbers {1042 ...... 1713} } ref
{ atomNumbers {406 ....... 1041} } }}harmonic { colvars dist
forceConstant 20.0 centers 5. # initial distance targetCenters
-5 # final distance targetNumStages 5 targetNumSteps 500000}*

Thanking you all in anticipation,

Regards,
Anirban Mandal

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