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#29368 - 02/21/12 03:25 AM vector orientation for methanol in solvent
prashant Offline
Forum Member

Registered: 04/12/10
Posts: 6
I have to calculate the orientational vector of methanol OH bond with respect to
the normal z axis. for calculating this i am trying to get the methanol in each frame but i don't understand how to get the bond distance for each of these selected methanol in each frame so that i can evaluate the COS(THETA).....need suggestion.....

Thanks in advance
Pras

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#29369 - 02/21/12 04:00 AM Re: vector orientation for methanol in solvent [Re: prashant]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4742
Loc: ~ 59N, 15E
correl.doc

One way to do this goes something like this (for one methanol):
correl
enter v1 vect xyz meoh 1 o meoh 1 h
traj firstu 101 nunit 1
mantime v1 normal
write v1 dumb time unit 200
* dummy title
*
end

The z-coordinate of v1 (4:th column written to unit 200) is cos(theta) for the OH of this methanol.

Note that if you used SHAKE during your simulation the O-H bond length is fixed to the value given in the parameter file (you can also measure it easily, by hand, using a molecular graphics program or the CHARMM commnand "Quick meoh 1 o meoh 1 h" (miscom.doc).
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#29583 - 03/20/12 04:57 AM Re: vector orientation for methanol in solvent [Re: prashant]
prashant Offline
Forum Member

Registered: 04/12/10
Posts: 6
Thanks a lot Lennart. i did it and it work well, but i write another script to do this calculation.

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