VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Thu Nov 19 2020 - 09:29:43 CST

If you are in graphics mode, start loading the frames and then disable or
delete the representation using graphics mode. The overhead required by the
graphics will be removed. Then when the trajectory is fully loaded recreate
the representation.

Alternatively use command line/script to load the trajectory which will
take the same time (almost) as the time required using the steps above.

If your time step and record frequency is too close you can choose to skip
some frames assuming that it doesn't result in a loss of useful
information.

Removing waters from a trajectory, if you are only interested in a protein
will also speed things us as the desolvated trajectory will be much small
smaller and hence will load faster.

Just some things to think about.

On Thu, 19 Nov 2020, 11:03 PM Raman Preet Singh, <
ramanpreetsingh_at_hotmail.com> wrote:

> 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
>
>
>