Anisotropic characteristics of unfolding dynamics and mechanical stability of tetrameric parallel G-quadruplex

This dataset include the data and input files used for the Steered MD (SMD) simulations and standard MD simulations done in the article (see the data availability section of the article). Note that the starting structure PDBs are in the Supporting Information of the article.

plumed_input.tar.gz: It has the plumed input files for all SMD simulations in this study, from which you can find the definition of the anchors, and the pulling setups. Note that the plumed input files for SMD with SPC/E water have suffix "spce".

top_gro.tar.gz: The topology and ".gro" files used for SMD simulations in Gromacs. Note that for the SMD systems with the same number of G-quartets but different pulling anchors (1-6/1-7/1-8), they share the same ".top" and ".gro" file, the difference of pulling anchors are defined in plumed files. Also note that the files used for SMD with SPC/E water have the suffix "spce".

distance_force.tar.gz: It includes the "COLVAR" files for each SMD simulation replicate (in total 45 runs). The SMD simulations with SPC/E water have suffix "spce". The header of these files are: "time x1 eRMSD_start RMSD_start pulling.force2 pulling.work pulling.bias". Here are more explanations of each column in these files:

time: simulation time (in picosecond)

x1: distance between the anchors (anchors are set in the corresponding plumed file, in nanometer)

eRMSD_start: eRMSD value to the starting structure (see: https://www.plumed.org/doc-v2.8/user-doc/html/_e_r_m_s_d.html)

RMSD_start: RMSD value to the starting structure

pulling.force2: The instantaneous value of the squared force due to this bias potential (in [kJ/(nm*mol)]^2, convert it to pN/mol, should do sqrt, and then *1.661)

work: The total work performed changing this restraint

bias: The instantaneous value of the bias potential

input.tar.gz: Contains the input files used for:

Minimization and equilibration (necessary before both standard MD and SMD)

Standard MD simulations

SMD simulations