Hi Everyone,
I’ve 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 ’T’ 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
