From: Anurag Sharma (Anurag.Sharma_at_my.ndsu.edu)
Date: Fri Jun 21 2013 - 20:47:47 CDT
Hi Norman,
I used langevinpiston algorithm to raise the pressure of the entire system to gring it to the room pressure. Now I like to calculate the strain on the sytem due to applied stresses. I am not sure how can achieve using this algorithm. I have attached a snapshot of the sytem in my last email.
Thanks
Anurag Sharma
________________________________
From: Norman Geist [norman.geist_at_uni-greifswald.de]
Sent: Thursday, June 13, 2013 1:56 AM
To: Anurag Sharma
Cc: Namd Mailing List
Subject: AW: namd-l: how to apply force SMD method on an anisotropic geometry
Hi Anurag,
if you mean pressure as force on the boundaries, this could be done using one of the barostat (langevinpiston or berendsen I guess) algorithms.
Also, have you thought about using dummy atoms to get such a plane that you talked about, or what exactly is the problem, what’s the molecules shape and where to you want to apply the force?
Norman Geist.
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
Dear all users,
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.
Thank in advance.
Anurag Sharma
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