From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Aug 29 2012 - 09:58:49 CDT
Hi Yi,
Do you have any sample script to do that.
Thanks in advance.
S
On Mon, Aug 27, 2012 at 2:40 PM, Wang Yi <dexterwy_at_gmail.com> wrote:
> 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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