<span style>Greetings Gromacs,</span><div style><br></div><div style>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. </div>
<div style><br></div><div style>So my questions are; is this behaviour related to the fact that my frame output occurs every 100ps? </div><div style>The rotations are actually discreet, so they may rotate back to their original positions, does this explain the decay?</div>
<div style>Is there a better way to characterise these sorts of rotation? <br><br clear="all"><div>relevent run parameters:</div><div><br></div><div><div>dt = 0.001</div><div>nsteps = 10000000</div>
<div>nstxout = 10000</div><div>nstvout = 10000</div></div><div><br></div><div>>300 monolayer molecules</div><div>OPLS, NPT</div><div><br></div><div>Any feedback would be appreciated! Thanks</div>
<div><br></div><div><br></div><div>Michael Plazzer</div><div>Applied Physics, School of Applied Science</div><div>RMIT</div></div>