Yes you can do it it, but of course the interpretation is up to you. It can
be helpful for comparing the trajectories.
On Mon, Nov 18, 2024, 7:44 AM Nikolay Kuzmich <
nikolay.kuzmich.weizmann.ac.il> wrote:
> Dear Carlos,
> Thank you for your reply.
> I meant the mean RMSDs from several trajectories.
> Now I started to doubt if it makes sense at all since each trajectory is a
> unique path from the starting structure.
> Kind regards,
> Nick
> ------------------------------
> *From:* Carlos Simmerling <carlos.simmerling.gmail.com>
> *Sent:* Monday, November 11, 2024 1:21 PM
> *To:* Nikolay Kuzmich <nikolay.kuzmich.weizmann.ac.il>; AMBER Mailing
> List <amber.ambermd.org>
> *Subject:* Re: [AMBER] Cpptraj: is it possible to perform 2D RMSD
> analysis from average data of several simulations?
>
> *Caution: External Sender. Do not click on links or open attachments
> unless you recognize the sender.*
>
> You can include multiple trajin filr. I am not sure what you mean by
> averaged. Since the axes of the plot are frame number or time, there is no
> averaging.
>
> On Mon, Nov 11, 2024, 5:35 AM Nikolay Kuzmich via AMBER <amber.ambermd.org>
> wrote:
>
> Dear Amber users and developers,
> I wanted to ask you if it is possible to get 2D RMSD matrix averaged from
> several independent production runs.
> Kind regards
> Nick
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Received on Mon Nov 18 2024 - 05:00:02 PST
