Apply torque with NAMD

From: George Patargias (gpat_at_bioacademy.gr)
Date: Tue Feb 12 2013 - 05:30:28 CST

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Hello

Sorry for posting about this again, but I got no reply.

I just wanted to know how can we apply a torque to a part of a system a
using NAMD.

Is this done through the rotating constraints? (flags rotConstraints,
rotConsAxis, rotConsPivot and rotConsVel options in the conf file)

Do we also need the SMD options in the conf file?

I am a bit confused because in this link

http://www.ks.uiuc.edu/Research/f1atpase/

it is mentioned "We use steered molecular dynamics (SMD) simulations to
apply a torque to F1..."

Thanks.

Dr. George Patargias
Postdoctoral Researcher
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece

Office: +302106597568

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