[AMBER] Minimizing Size of Membrane Simulation Box

From: Parker de Waal <Parker.deWaal.vai.org>
Date: Wed, 24 Sep 2014 01:05:57 +0000

Hi Everyone,

Iíve recently been working with some membrane bound simulations, built using the CHARMM-GUI membrane builder, and was wondering if there was a way to minimize the size of the simulation box with OPM database oriented proteins.

Specifically my system is a protein complex with a non-uniform shape, think íTí going through a a membrane, and the resulting CHARMM-GUI file is a large unoptimized rectangle that could afford to lose ~10 A on all sides while still providing sufficient buffering.

Is there a way to optimize the size of the membrane using the CHARMM membrane builder? Or will I need to experiment with VMD to build a more compact optimized system?

If anyone has any input on how to do this, or can provide alternatives, please let me know.

Best,
Parker

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Received on Tue Sep 23 2014 - 18:30:02 PDT
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