Author: Eichhorn, Catherine D.; Feng, Jun; Suddala, Krishna C.; Walter, Nils G.; Brooks, Charles L.; Al-Hashimi, Hashim M.
Title: Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch Document date: 2011_10_18
ID: kci1lkhj_12
Snippet: Simulation. REMD simulations were performed with the CHARMM simulation package (49) using the recently updated CHARMM27 nucleic acid force field (31, 32) and the MMTSB (50) tool set. Each REMD simulation comprised 40 replicas exponentially distributed over a temperature range from 278 K to 330 K, resulting in an average exchange acceptance ratio of 30%. Each replica was first equilibrated for 0.5 ns, restraining nucleotide heavy atoms, and subseq.....
Document: Simulation. REMD simulations were performed with the CHARMM simulation package (49) using the recently updated CHARMM27 nucleic acid force field (31, 32) and the MMTSB (50) tool set. Each REMD simulation comprised 40 replicas exponentially distributed over a temperature range from 278 K to 330 K, resulting in an average exchange acceptance ratio of 30%. Each replica was first equilibrated for 0.5 ns, restraining nucleotide heavy atoms, and subsequently run without any restraints for 10 ns, with exchange moves attempted every 0.5 ps.
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