[AMBER] umbrella box size for protein-protein

From: Fabian Glaser <fabian.glaser.gmail.com>
Date: Tue, 26 Nov 2019 11:38:39 +0200

Dear experts,

I am setting up a protein-protein complex system for which I would like to run umbrella sampling along the center of masses vector (my reaction coordinate), to compute the dissociation energy, etc. In order to allow a enough space during US, as the distance along the center of mass, COM-COM of proteins increase, I thought to use a cubic box, for which to set a larger dimension on the protein-protein intermolecular vector. Is that a good idea at all? Or should I stick with a very large octahedral box? (which will of course make run very very slowly)

If using a cubic box is indeed the right way to go, I don't’ find a way to align the box along the protein-protein COM axe (which is my reaction coordinate vector), and not the full box. I found the following command works to increase Z axe box size, but I cannot find the way to align Z to the COM-COM axes.

solvatebox com TIP3PBOX {10.0 10.0 50.0}

Can you please suggest a way to align the box with the complex in such a way that the Z axe is aligned to the protein-protein center of mass vector?

I would highly appreciate any suggestion wether this is the correct approach to go.

Thanks a lot!



Fabian Glaser PhD

Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Web http://bku.technion.ac.il/
Tel +972 (0) 4 8293701

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Received on Tue Nov 26 2019 - 02:00:02 PST
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