excluding non-bonded interactions between two proteins

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Wed May 04 2016 - 18:16:26 CDT

Hi all,

I know this comes up from time to time, but I’m not sure there is a good answer. I searched the list extensively, but might have missed something? I tried using alchemify to create non-bonded exclusion lists, but it’s too many (~1M) and NAMD crashes with the “low global exclusion count” error. While FEP might work, I’m pretty sure there’s no combination of values for alchElectLambdaStart and alchVDWLambdaEnd that maintain the scaling of interactions for BOTH proteins at 1 with the environment.

Any ideas?


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