How to find average structure at a fixed time gap, Does it have any physical significance?

User discussions
1

Is there any command to get an average frame from the MD output ?
For ex, if I have run a dynamics for 100ns, can i extract the average structure for every 25 ns , does it have any physical significance as I guess it will be far from reality…

Kindly clear my doubt…

2

Hi,

you can use gmx rmsf with the option -ox to get a pdb file with the average coordinates.
https://manual.gromacs.org/current/onlinehelp/gmx-rmsf.html

Note that the structure you get are an average, thus not a realistic structure.

Best regards
Alessandra

3

Thank you so much…
Let me try this out though its not meaningful.