Previous Thread
Next Thread
Print Thread
Page 1 of 2 1 2
CORREL: principal inertial axis reorientation
#4992 01/14/05 01:30 AM
Joined: Sep 2003
Posts: 8,499
rmv Online Content OP
Forum Member
OP Online Content
Forum Member
Joined: Sep 2003
Posts: 8,499
The following example illustrates some CORREL usage, calculating autocorrelation functions for the principal axis of the moment of inertia of a group of selected atoms, as well as that for an end-to-end vector.


* reorientation of the principal axis from moment of inertia tensor
* arg N == last file no.
*

! INIT FOR SUCROSE NEUTRON CONFIG IN CUBIC WATER BOX
stream initbox30.str

calc mxt @N * 100
calc tot @mxt / 4

correl maxt @mxt noupdate maxs 32
! VECTORS TO EXTRACT
enter pv inertia sele segid S end
enter ee vect xyz S 1 C4 S 2 C4
! STORAGE FOR CORR FXNS; ORDER OF DECLARATION MATTERS
enter ci1 zero
edit ci1 total @tot
enter ci2 dupl ci1
enter ce1 dupl ci1
enter ce2 dupl ci1

! OPEN THE INPUT TRAJ FILES, 1 THRU N
set num 1
set uni 31
label olp
open unit @uni write file name dyn@num.trj
incr uni by 1
incr num by 1
if num .le. @N goto olp

! PROCESS THE TRAJ FILES, FILE THE TIME SERIES WITH DATA
traj firstu 31 nunit @N

! NORMALIZE VECTORS AND COMPUTE P1 AND P2 AUTOCORR FXNS
mantim pv norm ! NORM
corfun pv pv p1 total @tot ! P1
mantim ci1 copy corr ! STORE RESULT (corr) IN ci1
corfun pv pv p2 total @tot ! P2
mantim ci2 copy corr ! STORE

mantim ee norm
corfun ee ee p1 total @tot
mantim ce1 copy corr
corfun ee ee p2 total @tot
mantim ce2 copy corr

! THE EDIT COMMAND COMBINES ci1 ci2 ce1 ce2; WRITTEN TO ONE FILE
edit ci1 veccod 4
open unit 12 write card name mireo.cor
write ci1 unit 12 dumb time
* dummy
*
end
stop


Rick Venable
computational chemist

Re: CORREL: principal inertial axis reorientation
rmv #4993 10/09/05 10:31 AM
Joined: Feb 2005
Posts: 7
K
Forum Member
Offline
Forum Member
K
Joined: Feb 2005
Posts: 7
Rick, would you please to add some explanations
how one should get all 3 rotational ACF?

thank you.

Re: CORREL: principal inertial axis reorientation
krupin #4994 10/09/05 01:55 PM
Joined: Sep 2003
Posts: 8,499
rmv Online Content OP
Forum Member
OP Online Content
Forum Member
Joined: Sep 2003
Posts: 8,499
We investigated that, and found that the interchange of the 2 minor axes was a severe problem with no easy algorithmic solution; these sudden non-physical shifts of 90 deg made computing correlation functions impractical for the molecules we were investigating. I suggesting picking surrogate vectors for the VECT time series type, and compute the time correlation function of those vectors instead.


Rick Venable
computational chemist

Re: CORREL: principal inertial axis reorientation
krupin #4995 10/09/05 02:47 PM
Joined: Sep 2003
Posts: 4,794
Likes: 2
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,794
Likes: 2
In recent versions (c31b1 and later I believe) there is an option to get all three principal axes in correl; the code that corrects for spurious interchanges does however have a couple of silly bugs (fixed in the next release), but as Rick points out it is not always possible to spot these swaps correctly (in particular if you are using a large SKIP value in the analysis). In our limited experience with small proteins axis swapping has not been a problem.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: CORREL: principal inertial axis reorientation
lennart #4996 10/09/05 03:56 PM
Joined: Sep 2003
Posts: 8,499
rmv Online Content OP
Forum Member
OP Online Content
Forum Member
Joined: Sep 2003
Posts: 8,499
With a reasonable interval between time points, it should be okay for large, fairly rigid macromolecules; it's more of a problem for short peptides, oligosaccharides, lipids, neat alkanes, neat ethers, etc.


Rick Venable
computational chemist

Re: CORREL: principal inertial axis reorientation
rmv #4997 02/03/09 06:10 PM
Joined: Jul 2004
Posts: 165
B
Forum Member
Offline
Forum Member
B
Joined: Jul 2004
Posts: 165
dear rick,
I got the following column for the P-N vector of the lipid head group. The 1st column should be a time, but i am not so sure about the 2nd and 3rd column?
thank you for your help.
0.000000 1.000000 1.000000
5.000000 0.971475 0.918035
10.000000 0.960319 0.888238
15.000000 0.951557 0.865780
20.000000 0.943885 0.846703
25.000000 0.937154 0.830445
30.000000 0.930919 0.815697
35.000000 0.925124 0.802287
40.000000 0.919751 0.790125
45.000000 0.914676 0.778877
50.000000 0.909856 0.768361
55.000000 0.905271 0.758557
60.000000 0.900799 0.749059

Re: CORREL: principal inertial axis reorientation
beginner #4998 02/03/09 06:30 PM
Joined: Sep 2003
Posts: 8,499
rmv Online Content OP
Forum Member
OP Online Content
Forum Member
Joined: Sep 2003
Posts: 8,499
They are the P1 and P2 time correlation functions, respectively; the latter is most often the one of interest for time decay.

Re: CORREL: principal inertial axis reorientation
rmv #4999 02/03/09 07:21 PM
Joined: Jul 2004
Posts: 165
B
Forum Member
Offline
Forum Member
B
Joined: Jul 2004
Posts: 165
thank rick,

could you please give me more hint?

one could estimate the correlation time by an exponential fit to the graph, right?
but my simulation time is still too short (50 ns) to get the decay to zero. how should I do to get the reasonable estimation to represent relaxation time for the molecule.

thank you.

Re: CORREL: principal inertial axis reorientation
beginner #5000 02/03/09 07:40 PM
Joined: Sep 2003
Posts: 8,499
rmv Online Content OP
Forum Member
OP Online Content
Forum Member
Joined: Sep 2003
Posts: 8,499
That vector does not have unrestricted motion in all directions, and should not decay to zero; it will have a long time plateau value, which can be interesting in some cases. For example, with the C-H vectors in lipids, the plateau value is the SCD value, i.e. the deuterium order parameter.

The relaxation time is not the decay to zero, but to 1/e (roughly 0.38).

For the P-N vector, the decay will likely be a multi-exponential; there a several types of motion that contribute, possibly on overlapping time scales. These are not rigid bodies, and this vector probably represents changes in rotamer states in the alpha chain as much as anything. The vector would not represent whole molecule motions much at all, as the head group and chain motions are fairly uncoupled.

Re: CORREL: principal inertial axis reorientation
rmv #5001 02/03/09 08:28 PM
Joined: Jul 2004
Posts: 165
B
Forum Member
Offline
Forum Member
B
Joined: Jul 2004
Posts: 165
thank you rick,

as I plan to monitor rotational motion in different part of the lipid molecule,i.e., head, glycerol backbone and the tails.

Based on what you say, C-H vector at a various position of the lipid tails would be more interesting to discuss than C-Cend of the tail. correct?

Re: CORREL: principal inertial axis reorientation
beginner #5002 02/03/09 08:35 PM
Joined: Sep 2003
Posts: 8,499
rmv Online Content OP
Forum Member
OP Online Content
Forum Member
Joined: Sep 2003
Posts: 8,499
The C-D bond order parameters (SCD) from deuterated lipids are possibly the most published expt and simulation data for bilayers, esp. for the chains.

Page 1 of 2 1 2

Moderated by  lennart, rmv 

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

PHP: 5.6.33-0+deb8u1 Page Time: 0.013s Queries: 36 (0.008s) Memory: 0.9963 MB (Peak: 1.1372 MB) Data Comp: Off Server Time: 2020-10-01 14:21:21 UTC
Valid HTML 5 and Valid CSS