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

From: Anurag Sharma (Anurag.Sharma_at_my.ndsu.edu)
Date: Fri Jun 21 2013 - 20:38:47 CDT

Hi Jerome,

     I do not want to apply forces to all atoms in the system but only on the surface atoms. My main concern is how to identify these surface atoms as they are in large no. and randomly arranged.

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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> 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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> 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.
>
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> 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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