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#18903 09/16/08 11:38 AM
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I would like to calculate the rotational motions of the lipid headgroups and their hydrocarbon chain tails by using correl facilities in charmm.

I would start from
set k 1
label elp
enter a@K vect z @K P @K N ! head
!enter b@K vect z @K c23 @K c43 ! sn1
!enter c@K vect z @K c33 @K c53 ! sn2
incr k by 1
if k le 224 goto elp

but I dont know how to get the profile out of this.
Thank you.

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rmv Online Content
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It depends on how you'd like to analyze and/or portray those motions; it isn't clear what you mean by "profile".

You probably want the complete vector, i.e. VECT XYZ as opposed to VECT Z to start with; then you can look at the reorientation time decay via CORFUN. I'm not sure whether P1 or P2 is more appropriate for this vector; that can depend on the available experiment data. I often compute both.

With VECT XYZ you can also compute various angles and their distributions, such as that wrt. the bilayer plane, and/or rotation around the bilayer normal vector. With VECT Z you have the difference in Z coordinates for the P and N atoms (and not much else).

Also, I've found it's usually best to include the SEGID for an 'atom-spec' in CORREL

Finally, you can also compute the principal axis from the moment of inertia for a group of atoms via the INERtia time series, and analyze that vector in the same ways (CORFUN, or angular history and distribution).

rmv #18905 09/17/08 02:13 PM
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Thank you rick,

To compute the correlation function, I did

set k 1
label elp
enter a@K vect xyz @K P @K N ! head
!enter a@K vect xyz @K c21 @K c45 ! sn1
!enter a@K vect xyz @K c31 @K c55 ! sn2
!enter a@K vect xyz @K c2 @K c3 ! glycerol
incr k by 1
if k le 224 goto elp
! STORAGE FOR CORR FXNS; ORDER OF DECLARATION MATTERS
enter avv zero
edit avv total @tot
enter abv dupl avv

! OPEN THE INPUT TRAJ FILES

open unit 31 file name lip.dcd
traj firstu 31 nunit 1 skip 2500

set k 1
label pol
mantim a@K norm
corfun a@K a@K p1 total @tot
mantim avv copy corr
corfun a@K a@K p2 total @tot
mantim abv copy corr
incr k by 1
if k le 224 goto pol
! THE EDIT COMMAND COMBINES avv abv; WRITTEN TO ONE FILE
edit avv veccod 2
open unit 12 write card name data.dat
write avv unit 12 dumb time
* dummy
*
end
stop
It went well.

However, I am not so sure how i can get the distribution around the bilayer normal or the bilayer plan.
It seemed to me that I can not say only "VECT Z" or "VECT XY" on the command line.

Thank you in advance for your help.

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rmv Online Content
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Each analysis may require a different approach, and may be best done with some external processing (another program).

I have some scripts for computing the angle wrt. the bilayer normal (Z axis) with some simple geometry, and averaging the distributions from each molecule. I'll put them in the Script Archive within the next few days.

For the radial distribution representing rotation around the Z axis, I simply write the VECT XYZ time series data for the molecules to a file, and use a Fortran program for the analyses, mostly graphic.

rmv #18907 09/19/08 07:16 AM
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thank you very much, rick.

rmv #18908 11/26/08 08:17 PM
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I forgot about this; I have posted an example for the angle of the P-N vector of PC headgroups in the Script Archive.


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