[AMBER] Accounting for PBC in Density Plots

From: An Ta <anta.mymail.mines.edu>
Date: Mon, 6 Jul 2020 12:44:06 -0500

Dear AMBER users and colleagues,

I have been attempting to correct multiple density profiles for a biphasic
system. The simulations were performed with PBC on a system that contains a
water-dodecane solvent and two specific surfactants. Currently, I am trying
to account for PBC in the density analyses since I am observing "erroneous"
peaks at the edge of my box. The density profiles were calculated such that
the mass density of my constituents are assessed in reference to the
z-dimension of my box. I have tried the unwrap and autoimage action
commands and the profiles still possess the erroneous peaks at the edge of
the box.

I have included one of the density profiles that I am trying to correct for
in this thread. This specific plot was calculated with a trajectory that
has neither been unwrapped or autoimaged. Even so, density plots calculated
with the new trajectories that were unwrapped or autoimaged looked
similar to the one provided. Thank you for your consideration and any

*An T. Ta *
Department of Chemistry | Ph.D. Candidate
Coolbaugh Hall | Room 118
Golden, CO 80401
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Received on Mon Jul 06 2020 - 11:00:04 PDT
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