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vector orientation for methanol in solvent
#29368 02/21/12 08:25 AM
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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

Re: vector orientation for methanol in solvent
prashant #29369 02/21/12 09:00 AM
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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
Re: vector orientation for methanol in solvent
prashant #29583 03/20/12 08:57 AM
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Thanks a lot Lennart. i did it and it work well, but i write another script to do this calculation.


Moderated by  lennart, rmv 

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