[AMBER] periodic boundary conditions

From: Neha Gandhi <n.gandhiau.gmail.com>
Date: Tue, 28 Feb 2017 11:19:56 +1000

Dear List,

I have a system with hydroxyapatite (HAP) and the protein is place 10 A
around an axis parallel to the HAP surface (i.e. above HAP surface in Z
direction). Interface force field and ff14SB are applied to HAP and protein
respectively. The system is solvated using TIP3PBOX in two different ways

1. There is a 25 A layer of water above the protein and no water is present
below the HAP surface.
2. The system (HAP+protein) is solvated using the standard solvatebox
protocol with 10A distance (the distance between any box edge and any atom
of solute).

The simulations are carried out using a cutoff of 10 A. In case 1, upon
visualization of the trajectory that there are pbc issues with the system
with one layer of HAP appearing on the other side of the box (i.e. it
resembles that the protein is between two HAP surfaces) despite a bigger
box size.

I was wondering how periodic boundary conditions are dealt in AMBER (such
as in case 1). Is this ok or something is seriously wrong? If wrong, what
is the procedure to solvate this system and avoid pbc issues?

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Received on Mon Feb 27 2017 - 17:30:03 PST
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