[gmx-users] characterising monolayer molecule rotation
Michael Bernard Plazzer
s3225169 at student.rmit.edu.au
Mon May 21 04:55:01 CEST 2012
Long time reader, first time poster. I am modelling monolayer/water systems
composed of long-chain fatty alcohols and have observed the molecules to
rotate around their long-axis, I would like to characterise this using
GROMACS. I have had some success calculating the rotational correlation
function using g_rotacf where the triplet was chosen as the top, middle and
bottom carbons of, for example, octadecanol (this is a particularly
elongated triangle, if that makes a difference, 18 Carbons long). Over a
10ns run, this produces a C(t) that decays very quickly to ~0.4, in less
than 250ps, after which the decay is very slow and does not reach zero.
So my questions are; is this behaviour related to the fact that my frame
output occurs every 100ps?
The rotations are actually discreet, so they may rotate back to their
original positions, does this explain the decay?
Is there a better way to characterise these sorts of rotation?
relevent run parameters:
dt = 0.001
nsteps = 10000000
nstxout = 10000
nstvout = 10000
>300 monolayer molecules
Any feedback would be appreciated! Thanks
Applied Physics, School of Applied Science
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