From: Alessio Alexiadis (sersunzo_at_yahoo.com)
Date: Fri Jul 13 2007 - 13:13:23 CDT
I run some simulation of water in carbon nanotubes of different size [from (8,2) to (58,0)] immersed in a much larger water box using a flexible TIP3P water model (the same used in the NAMD nanotube tutorial) at 300K (Langevin in dynamic) and 1bar (Langevin in Piston). At the end of the simulation (1ns) I checked the average water angle inside the nanotube and it is approximately 102 degrees for all the nanotubes. The angle distribution is a well-shaped Gaussian with average 102 and standard deviation approx 3 degrees. I also checked the angle of water molecules located far from the nanotube (distance 20 Å) but the average angle is still the same. I was expecting to see something close to 104.52 degrees (at least in the larger nanotubes) so I’m wondering if anybody never heard of this phenomenon or I just did something wrong.
Thanks in advance
PS. Do you know any paper, where the average angle for flexible water models is calculated?
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