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#27023 - 04/04/11 02:23 PM Re: bilayer chain tilt [Re: rmv]
jeremy adler Offline
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Registered: 02/23/11
Posts: 31
Hi Dr. Venerable,

why not just use coor helix?

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#27024 - 04/04/11 02:55 PM Re: bilayer chain tilt [Re: jeremy adler]
rmv Online   content

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Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
COOR HELIX does not process trajectory files; in general, an analysis using CORREL will be much more efficient than a loop over frames.

There often can be a couple different ways to do a particular analysis, and sometimes it's useful to try more than one and compare the results.
_________________________
Rick Venable
computational chemist


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#27026 - 04/04/11 03:07 PM Re: bilayer chain tilt [Re: rmv]
lennart Online   content

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Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
There is a helix timeseries in correl, but this is (just as COOR HELIx) intended for helical structures, and may not be appropriate for a fatty acid hydrocarbon tail.
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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#27030 - 04/04/11 03:46 PM Re: bilayer chain tilt [Re: lennart]
rmv Online   content

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Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
In either case, it should be noted that the tilt calculation is only meaningful when the chains are fairly ordered, such as more gel-like states.
_________________________
Rick Venable
computational chemist


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#34530 - 11/02/14 01:08 PM Re: bilayer chain tilt [Re: rmv]
shanKim Offline
Forum Member

Registered: 01/02/14
Posts: 8
Dear rick,

Hello, I have a question:
Actually you know, DPPC lipid has 16 carbons in each of chain.
But, script in this archive can calculate tilt angle from C3 to C13.
Are they have specific reason?
Why you don't calculate from C1 to C16?

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#34531 - 11/02/14 01:32 PM Re: bilayer chain tilt [Re: rmv]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
The free ends of the chains are highly disordered, and the upper ends near the glycerol are influenced by the ester binding geometry and headgroup packing.
_________________________
Rick Venable
computational chemist


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#34600 - 11/28/14 12:36 AM Re: bilayer chain tilt [Re: rmv]
shanKim Offline
Forum Member

Registered: 01/02/14
Posts: 8
Dear Rick,

Thanks, I understood that in case of C3.
However, I think that setting the end to end vector (C3-C16) is more reasonable to check the tilt angle.
Is it does not matter if all values are calculated from C3 to C13?


Edited by shanKim (11/28/14 12:37 AM)

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#34601 - 11/28/14 12:12 PM Re: bilayer chain tilt [Re: rmv]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
What matters most is that you are consistent in your methods, and clearly state what you've done in reports and publications.

Because of the flexibility of the free chain ends, I do not agree that using the terminal methyl is more reasonable; if you are concerned, do the calculation both ways and see how much difference it makes.
_________________________
Rick Venable
computational chemist


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