Topic Options
#36970 - 05/21/18 09:42 AM rmsd calculation
abir Offline
Forum Member

Registered: 04/18/18
Posts: 6
Dear all, I am very new to charmm. Is it possible to calculate rmsd value of a simulation run without invoking correl command in charmm?
please help in this regard...

Top
#36971 - 05/21/18 11:44 AM Re: rmsd calculation [Re: abir]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
Yes, but CORREL is usually the most efficient method when dealing with simulation trajectories.

The COOR RMS command (corman.doc) will compute the RMS difference between MAIN and COMP coordinate sets, and COOR ORIENT RMS will first align the the two coordinate sets, then compute the RMS. This could be done in a loop over frames; see the Script Archive forum.

The atom selection(s) and reference structure are important considerations for either approach.
_________________________
Rick Venable
computational chemist


Top
#36972 - 05/22/18 07:19 AM Re: rmsd calculation [Re: abir]
abir Offline
Forum Member

Registered: 04/18/18
Posts: 6
Thanks Rick.

Top

Moderator:  John Legato, lennart