Hi.
We are getting ready use the NEB method for a large conformational change in a large system. We have completed the NEB tutorial and prepared the starting point/endpoint input files. I have few questions.
Our total system size protein + solvent is ~45,000 atoms and our protein is 373 residues. The conformational change is complex and involves, among other things, the separation of 2 beta strands and the movement of a loop across nearly 60 angstroms. The tutorial was obviously optimized for a much smaller system.
1. What's a good estimate for how long we should equilibrate at each temp. during the simulated annealing? Can we use the annealing schedule in the tutorial as a guide, or do we need to try something totally different for a system this size?
2. Is it recommended to use apply NEB forces to the entire protein?
3. We were thinking of starting with half the replicas at the starting point and half at the endpoint and letting the NEB method find the path. Might it be better to generate a candidate path with targeted MD first?
Thanks.
Patrick L. Wintrode
Assistant Professor
Department of Physiology & Biophysics
Case Western Reserve University
Cleveland, OH 44106
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Received on Wed May 25 2011 - 08:00:04 PDT
