Previous Thread
Next Thread
Print Thread
#28868 12/07/11 09:42 PM
Joined: Feb 2011
Posts: 31
J
Forum Member
OP Offline
Forum Member
J
Joined: Feb 2011
Posts: 31
Hi

When i used mantime to get the dotproduct of two vectors (x y z) it outputted another vector of the same dimension (x y z)- should i just concern myself with the x column or did i do something wrong?

the code:

correl maxtim 1000000 maxa 900 maxs 10
enter s1 atom xyz sele segid proa end mass
enter s2 atom xyz sele segid prob end mass
open unit @u read file name ../dimer.@k.wt/restart.run.dcd
traj firstu @u nunit 1 stop 46000000 skip 500
mantim s2 mult -1.0
mantim s1 add s2
mantim s1 dotp s1
mantim s1 sqrt s1
open write unit 1 card name com.wt.@k.dat
write s1 unit 1 dumb time
* dumb
*
end
close unit 1


Thanks

Jeremy

Joined: Sep 2003
Posts: 4,861
Likes: 10
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,861
Likes: 10
According to correl.doc:
mantime Q DOTP Q2
results in
Q(T) x-comp=Q(T).Q2(T)
and
Q2(T)x-comp=angle Q(T) vs Q2(T) degrees

I'm not sure your "mantime s1 sqrt" is meaningful here (and the second s1 is syntactically incorrect).
To get the distance between the centers of your selections you may try the distance time-series (enter d dist sele end sele end), or with your subtraction of s2 from s1 use mantim s1 abs which should return the length of the vector in the x-component (not well documented).
skip 500 is perhaps a bit too frequent for such a long trajectory?


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Joined: Sep 2003
Posts: 8,623
Likes: 24
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,623
Likes: 24
Those commands don't change the number of data columns allocated for a time series, so "WRITE S1" will write out all 3 columns. However, there may be an issue, since correl.doc suggests that the x component of BOTH time series is modified, which implies they should be different time series. I suggest changing the above from

mantim s1 add s2
mantim s1 dotp s1
mantim s1 sqrt s1

to

mantim s2 add s1
mantim s1 dotp s2
mantim s1 sqrt
edit s1 veccod 1

The last line changes s1 to a single column time series of the x component. As Lennart notes, however, it's not completely clear what property you are trying to compute.


Rick Venable
computational chemist


Moderated by  lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.5
(Release build 20201027)
Responsive Width:

PHP: 7.3.31-1~deb10u1 Page Time: 0.008s Queries: 20 (0.005s) Memory: 0.7381 MB (Peak: 0.7836 MB) Data Comp: Off Server Time: 2022-12-04 21:12:14 UTC
Valid HTML 5 and Valid CSS