Previous Thread
Next Thread
Print Thread
rdf using coor anal
#38373 11/22/21 03:05 AM
Joined: Dec 2018
Posts: 14
J
Forum Member
OP Offline
Forum Member
J
Joined: Dec 2018
Posts: 14
I am trying to study rdf of my system. My script is something like this:

coor anal select type ION end -
xref @xsite yref @ysite zref @zsite -
firstu 51 nunit 1 begin ?start skip ?skip -
isdist 41 -
rsph 999.9 mgn 800 dr 0.2 -
dens 0.001

The trajectory file contains 500ns data. I also run the script for every 100ns data by assigning the "begin" and "stop" in the third line such as "firstu 51 nunit 1 begin 10000000 stop 20000000 skip ?skip -".
I thought the rdf using all 500ns should be the average of the five 100ns rdf. However, although the five 100ns rdf plots are similar, their average is very different from the 500ns one. I even see a peak not present in any of the 100ns plots appears in the 500ns plot (within r<1). I am quite confused. Can anyone give me some hint? isn't rdf the average of rdf from each frame?

thank you very much.
james

Re: rdf using coor anal
jamesmao #38374 11/22/21 05:13 PM
Joined: Sep 2003
Posts: 4,830
Likes: 3
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,830
Likes: 3
Strange, the partial rdfs should sum up to the overall, as you expect. One thing that could confuse the issue is periodic boundary conditions, in particular for something like ions that I assume are spread out all over you system. COOR ANAL can handle some basic PBCs, but your command does not request this.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: rdf using coor anal
lennart #38375 11/22/21 07:01 PM
Joined: Dec 2018
Posts: 14
J
Forum Member
OP Offline
Forum Member
J
Joined: Dec 2018
Posts: 14
thanks Lennart. Turns out I made a silly mistake: 100ns is 100000000 instead of 10000000!

Re: rdf using coor anal
jamesmao #38376 11/23/21 07:22 PM
Joined: Sep 2003
Posts: 4,830
Likes: 3
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,830
Likes: 3
Good! Honest mistake, rather. As long as you don't repeat it and expect a different outcome you're OK, loosely quoting A. Einstein (a physicist of some fame a hundred years ago).
Having written parts of the underlying code, and used it a lot, I would like to point out that coor anal is not quite as bad as it may sound.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: rdf using coor anal
jamesmao #38377 11/27/21 11:20 PM
Joined: Dec 2018
Posts: 14
J
Forum Member
OP Offline
Forum Member
J
Joined: Dec 2018
Posts: 14
Since I only need local rdf around a specific site, I did not try PBC. Will give it a try later. BTW, what are other options/modules for rdf analysis in charmm besides coor anal? thanks.

Re: rdf using coor anal
jamesmao #38378 11/28/21 09:30 PM
Joined: Sep 2003
Posts: 8,582
Likes: 11
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,582
Likes: 11
If the site can be near a unit cell boundary, then you should use PBC or else under-counting can occur.

The HIST feature of COOR DISTance can be used to compute g(r) in a loop over frames, but it is much less efficient than using COOR ANAL and not recommended for general use. The COOR DIST approach does offer greater flexibility, including the ability to process each frame before accumulating histogram data, but is more cumbersome to use and significantly slower.


Rick Venable
computational chemist

Re: rdf using coor anal
jamesmao #38379 11/29/21 06:29 PM
Joined: Sep 2003
Posts: 4,830
Likes: 3
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,830
Likes: 3
COOR ANAL only supports very basic PBC. An alternative approach is to preprocess the trajectory and recenter each frame with the site of interest at the center. COOR MERGE RECENTER.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: rdf using coor anal
lennart #38382 12/07/21 03:22 PM
Joined: Dec 2018
Posts: 14
J
Forum Member
OP Offline
Forum Member
J
Joined: Dec 2018
Posts: 14
Hi Lennart, what do you mean "very basic PBC"? do you mean the geometry of the box? thanks.


Moderated by  lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 7.3.31-1~deb10u1 Page Time: 0.010s Queries: 30 (0.008s) Memory: 0.7508 MB (Peak: 0.8126 MB) Data Comp: Off Server Time: 2021-12-08 00:45:34 UTC
Valid HTML 5 and Valid CSS