Re: NAMD pulling one domain

From: Wang Yi (dexterwy_at_gmail.com)
Date: Mon Aug 27 2012 - 14:40:22 CDT

Use the Collective Variable function of NAMD. And in the atom selection entry, include the entire domain in the selection, so that you're pulling the CoM of that domain.
___________________________

Yi (Yves) Wang
Duke University

On 2012-8-27, at 下午3:36, snoze pa wrote:

> Dear NAMD users,
>
>
> I am working on a multi domain protein. Protein domains are similar to immunoglobin but instead of pulling one residue( i.e applying pulling force at one residue) i want to pull one complete domain. Is it possible using SMD in NAMD? So far I am trying following protocol:
>
> 1. Calculate center of mass (CM) of a domain of interest and then pull the CM in desired direction.
>
> Is this approach is correct?
>
> Thank you very much for your attention.
>
> S
>
>

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