DOI: 10.17863/cam.69048
title: Research data for MD Simulations of RNA CUG repeats

description: General Notes: If the file has an extension .gz, unzip it first. If the file has .tar extension, untar it first. In the pathway analysis, binary files were produced with OPTIM and PATHSAMPLE compiled with NAG version 5.2 (64 bit) fortran compilers.
description: 3xCUG The MD simulation is 1 microsecond long. In this trajectory file, structures were extracted from the original MD trajectory at each 1 nanosecond intervals yielding 1000 structures.
description: infinite_3CUG_anti_anti The MD simulation is 0.5 microsecond long. In this trajectory file, structures were extracted from the original MD trajectory at each 1 nanosecond intervals yielding 500 structures.
description: infinite_3CUG_syn_anti The MD simulation is over 600 nanosecond long. In this trajectory file, structures were extracted from the original MD trajectory at each 1 nanosecond intervals yielding 605 structures.
description: rCCGCUGCGG_pmf This directory includes umbrella sampling data of (chi, pseudtorsion) analysis. There are 1296 files corresponding to the results of 1296 umbrella sampling MD simulations. Each file includes 25K (chi, pseudtorsion) data points extracted at 80 fs intervals from the umbrella sampling results. The columns in each file corresponds to the MD step, chi, and pseudotorsion angles, respectively.
description: rCCGCUGCGG_pmf_tor1_tor2 This directory includes umbrella sampling data of (pseudtorsion1, pseudtorsion2) analysis. There are 1296 files corresponding to the results of 1296 umbrella sampling MD simulations. Each file includes 25K (pseudtorsion1, pseudtorsion2) data points extracted at 80 fs intervals from the umbrella sampling results. The columns in each file corresponds to the MD step, pseudtorsion1, and pseudotorsion2 angles, respectively.
description: temp_jump_experiment This directory includes temperature jump MD results (prmtop and MD trajectory files). Initial structures are either in anti-anti or syn-anti conformations. For each case, 10 independent temperature jump MD simulations were done. In each temperature jump MD, the temperature is gradually increased from 300 to 400 K in the first 20 ns. Another 19 ns MD were run at 400 K. In the trajectory files, structures were extracted from the original MD trajectories at each 1 nanosecond intervals yielding 39 structures for each case.
description: sample_md.input This is a sample sander/pmemd MD input file used in producing the MD trajectories.
description: sample_umbrella_sampling_files This is a file displaying sample scripts/files used in umbrella sampling calculations.
description: pathway_database This directory contains the converged databases for the RNA CUG repeat which was used for the rate constant calculations, as well as the creation of the disconnectivity graphs. NAG version 5.2 (64 bit) was used to compile OPTIM and PATHSAMPLE; thus, to make sure that the binary files provided can be analyzed, compile OPTIM and PATHSAMPLE with NAG version 5.2 (64 bit). (1) min.data -&gt; database of minima (2) ts.data -&gt; database of transition states (3) odata.connect -&gt; Input file for running OPTIM connections (4) pathdata -&gt; PATHSAMPLE input file (5) coords.prmtop -&gt; AMBER topology file (6) coords.inpcrd -&gt; AMBER coordinate file (7) min.in -&gt; AMBER specific input file for computing single point energies (8) min.A -&gt; syn-anti conformation (9) min.B -&gt; anti-anti conformation Running PATHSAMPLE with the current keywords will compute the rate constant for anti-anti syn-anti conformational transition, at a regrouping threshold of 2.0 kcal/mol and temperature of 300 K (0.596 in units of kcal/mol). For sampling specific keywords please refer to the PATHSAMPLE and OPTIM user manuals. (See http://www-wales.ch.cam.ac.uk/PATHSAMPLE/ and http://www-wales.ch.cam.ac.uk/OPTIM/). For further queries please email Prof David J. Wales (dw34 at cam.ac.uk).
description: This work was supported by the ERC, EPSRC, NIH, National Science Foundation, and Muscular Dystrophy Association