VMD-L Mailing List

From: Smith, Harper E. (smith.12510_at_buckeyemail.osu.edu)
Date: Thu Nov 19 2020 - 09:02:54 CST

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