[AMBER] Questions about Steered MD in Amber

From: Vu Truong <vutruong.lsp.gmail.com>
Date: Thu, 14 Jan 2016 13:10:59 -0700

Hi All,

I have several questions regarding to the Steered Molecular Dynamics
simulation in Amber package, which really needs your help.

1. Can we apply the external force into a system, for example, a water box
in the specific direction +z or -z by using Amber?

2. I actually have found that Amber also has the Steered MD method.
However, I am confused if that external force can be the force applied in a
specific direction? Also, does the parameter *iat *in input mdin file, for
example I will set 1 and 99, mean that the force will be applied between
atom 1 and atom 99. Or does it mean among the atom 1 to atom 99?

3. As I said, I am trying to apply the external force in a specific
direction +z /-z for my water box system. So any your advice how I can
proceed that idea is highly appreciated from me.

Thank you so much.

Vu T.
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Received on Thu Jan 14 2016 - 12:30:04 PST
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