VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Nov 19 2020 - 15:14:08 CST

Also, especially when working with large trajectories, it is good to be in
the habit of adding
waitfor all
to your load commands. This is especially important in scripting, as
otherwise the molfile load command will not block, and you'll get only
partial analysis of the trajectory.
Best,
Peter

On Thu, Nov 19, 2020 at 11:49 AM Smith, Harper E. <
smith.12510_at_buckeyemail.osu.edu> wrote:

> Hi Raman,
>
> This doesn't answer your question, but do you really need the RMSD of all
> 100,000 frames? Just load every few frames and calculate the RMSD of those.
> When loading data into molecule, change stride to e.g. 100.
>
> Best,
> Harper Smith
> ------------------------------
> *From:* owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of
> Raman Preet Singh <ramanpreetsingh_at_hotmail.com>
> *Sent:* Thursday, November 19, 2020 9:35 AM
> *To:* vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> *Subject:* vmd-l: Trajectory analysis without loading all frames
>
> Dear All,
>
> I did a fairly long simulation in Gromacs. The trajectory has 100,000
> frames. Loading of all frames takes several minutes and the waiting time
> can be annoying. When I look at RMSD using RMSD Tool while the frames are
> still loading, it shows RMSD of only those frames which have been loaded
> till that time.
>
> Is there a way to avoid the wait and calculate the RMSD of all frames?
>
> Thanks
>
> Raman
>
>
>