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 Re: Time series of Avg dist of Phos&Center of micelle
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Joined: Oct 2012
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OP
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Joined: Oct 2012
Posts: 24 |
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.
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Re: Time series of Avg dist of Phos&Center of micelle
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Joined: Sep 2003
Posts: 8,543 Likes: 3
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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
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Re: Time series of Avg dist of Phos&Center of micelle
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Joined: Oct 2012
Posts: 24
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OP
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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.
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Re: Time series of Avg dist of Phos&Center of micelle
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Joined: Sep 2003
Posts: 8,543 Likes: 3
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Joined: Sep 2003
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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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