Hi all,
I'm studying a conformational change in a large protein. Using implicit solvent, the system size is ~5,000 atoms (45 kD protein). Crystal structures are available for both the start and end states. The conformational change is quite large: one part of the protein moves nearly 40 angstroms, and most of the structure moves somewhat in response, so it's not clear that forces can be applied to only part of the system.
I'm working through the NEB tutorial now, but before I invest too much time, I want to check that I'm not wildly overestimating the size of the systems that the NEB method can realistically handle. I have access to a reasonably large computing cluster with ~1,200 processors.
Based on the above, does this sound like a feasible application of NEB?
Thanks.
Patrick L. Wintrode
Department of Physiology & Biophysics
Case Western Reserve University
Cleveland, Ohio, 44106
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Received on Thu Oct 07 2010 - 18:00:03 PDT
