RE: AW: how to apply force SMD method on an anisotropic geometry

From: Anurag Sharma (Anurag.Sharma_at_my.ndsu.edu)
Date: Thu Jun 13 2013 - 09:41:24 CDT

Hi,

    Yes Normen I am using pressure as force on the boundaries. I have attached a snapshot of my model with this mail. You can see in the snapshot that water atoms at the boundries are unevenly distributed. Due to their large no. I can not identify individual atoms hence I am thinking of putting them in a box and then apply force on the box boundries. Would this be a correct method to calculate stresses in the system.

Thanks

Anurag Sharma

________________________________________
From: Jrme Hnin [jerome.henin_at_ibpc.fr]
Sent: Thursday, June 13, 2013 2:54 AM
To: Norman Geist
Cc: Namd Mailing List; Anurag Sharma
Subject: Re: AW: namd-l: how to apply force SMD method on an anisotropic geometry

Hi Anurag,

If you want to apply custom forces to all atoms in the system, it is typically most efficient to script them as tclBC (Tcl boundary conditions).

Cheers,
Jerome

----- Original Message -----
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> Hi Anurag,
>
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> if you mean pressure as force on the boundaries, this could be done
> using one of the barostat (langevinpiston or berendsen I guess)
> algorithms.
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> Also, have you thought about using dummy atoms to get such a plane
> that you talked about, or what exactly is the problem, whats the
> molecules shape and where to you want to apply the force?
>
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>
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> Norman Geist.
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> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Anurag Sharma
> Gesendet: Mittwoch, 12. Juni 2013 22:40
> An: namd-l_at_ks.uiuc.edu
> Betreff: namd-l: how to apply force SMD method on an anisotropic
> geometry
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>
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> Dear all users,
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> I am working on a solvated model (protein surrounded by water
> molecules) which has anisotropic geometry. I am trying to apply
> force constant method (SMD) to calculate stresses and modulus of the
> system. In force constant method one applies force on individual
> atoms placed in a layer but due to anisotropic geometry I don't know
> how can I achieve this.
>
>
> Another possible way to calculate stresses is to put solvated system
> in a box and then apply force on the boundaries of that box. Is
> there any method in NAMD which I can use here.
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> Thank in advance.
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> Anurag Sharma

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