From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Wed May 04 2016 - 19:04:43 CDT
I just tried it, but “LES flag must be less than or equal to lesFactor”, meaning that the potentials will be scaled regardless.
It’s fine if there’s no “trick” for this; I just thought with as often as it comes up, there was something I had overlooked. I changed a couple lines in NAMD back in 2007 or so to do it, but that approach I used then wouldn’t even work now.
> On May 4, 2016, at 7:41 PM, Peter Freddolino <petefred_at_umich.edu> wrote:
> Could you hack LES to do this? How involved it would be depends on whether or not the two proteins are identical…
>> On May 4, 2016, at 7:16 PM, JC Gumbart <gumbart_at_physics.gatech.edu> wrote:
>> 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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