Greetings Gromacs, 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 OPLS, NPT Any feedback would be appreciated! Thanks Michael Plazzer Applied Physics, School of Applied Science RMIT
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