Keep it Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with Gromacs
نویسندگان
چکیده
منابع مشابه
Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS
We describe a versatile method to enforce the rotation of subsets of atoms, e.g., a protein subunit, in molecular dynamics (MD) simulations. In particular, we introduce a "flexible axis" technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation. A variety of useful rotation potentials were implemented for the GROMACS 4...
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1Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden, 2Dept. Theoretical Physics, KTH Royal Institute of Technology, 10691 Stockholm, Sweden, 3 Theoretical and Computational Biophysics Dept., Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany 4Center for Biomembrane Research, Dept. Biochemistry & Biophysics, Stockholm University, SE...
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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2012
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2011.11.927