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

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Mar 26 2018 - 07:01:01 CDT

Dear Anirban Mandal,

The natural companion of the *distanceZ* coordinate is *distanceXY*. You
could use it to restrain the horizontal distance between the two sheets to
be close to zero with the upperWall and upperWallConstant parameters.

Best,
Jerome

On 26 March 2018 at 12:04, ANIRBAN MANDAL <
anirban.mandal_at_msc2015.iitgn.ac.in> wrote:

> 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:
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> *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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