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Re: Time series of Avg dist of Phos&Center of micelle
swmmr1928 #32403 08/13/13 05:50 PM
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I am getting a good result.

Since the psf contains water and DPC, then I should not use ?nres because it include waters.

However the timeseries is still influenced by the intermittent breakup by reaching the boundary of the unit cell.
But it is easier to exclude those values.

Re: Time series of Avg dist of Phos&Center of micelle
swmmr1928 #32404 08/13/13 08:48 PM
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The problem is that the COM coordinates will also be a bit off because of lipids hopping across the unit cell due to image centering.


Rick Venable
computational chemist

Re: Time series of Avg dist of Phos&Center of micelle
swmmr1928 #32414 08/16/13 01:39 AM
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Yes, but if I can distinguish the snapshots that this is occurring and not include them it will be alright, right?
I can't upload the excel format, but heres a screenshot.

[img:right]http://imgur.com/D8DSrME[/img]

Last edited by swmmr1928; 08/16/13 01:40 AM.
Re: Time series of Avg dist of Phos&Center of micelle
swmmr1928 #32425 08/16/13 07:27 PM
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If you only include coordinate sets where the micelle is intact, then I believe you should get a reasonable estimate of the average radial distance of each P atom from the center of mass.


Rick Venable
computational chemist

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