DOI: 10.5281/zenodo.14232873
title: REMD trajectory of VPAA assemblies at 300K 1microsconds

description: V-shaped polyaromatic amphiphiles (VPAA) are aromatic micelles, amphiphilic molecules with anthracene panels aligned in a V-shape.

Microseconds molecular dynamics simulations show that VPAAs spontaneously self-assemble and disassemble in water, and at equilibrium, with size distributions of 5–7 and 4–6 for VPAA1 and VPAA2 at equilibrium, respectively.

This dataset is a trajectory for investigating the nature of the equilibrium distribution of VPAA assemblies. All-atom simulations (~60,000 atoms) of aqueous systems containing 27 molecules of two types of VPAA were performed. The two VPAAs are designated VPAA1 and VPAA2 and differ only in their hydrophilic groups (See attached figure(a)).

To obtain equilibrium samplings, the trajectory was subjected to equilibrium sampling at 1 atm for 1 microsecond by replica-exchange MD. Snapshots were recorded every 100 ps and non-aromatic carbon atoms were striped. The molecules were divided into assemblies, where molecules are defined as belonging to the same assembly if the nearest-neighbor distance of their aromatic carbon atoms is less than 5 Å. Note that due to the nature of the replica exchange method, the time series of the data has no physical meaning. Data only includes the last 900 ns processed.

The detailed simulation settings are as follows: The force fields used were gaff and TIP3P, and some corrections were made using quantum mechanical calculations. First, energy minimizations of the systems were performed in 1,000 step. Then, the systems were heated up from 0 K to 300 K in 2 ns, and equilibrated for 2 ns at 300 K in NVT ensemble. NPT simulations for 10 ns at 300 K then followed to determine the simulation box sizes. After equilibrations, the box sizes were nearly constants and cubic, and they were determined to be 82.01 Å per side for VPAA1 and 82.07 Å per side for VPAA2, respctively. Finally, we heated up the systems to 1,000 K and then cooled down them to 300 K in NVT ensemble (equilibration at 300 K for 2 ns, heating up from 0 K to 300 K in 2 ns, equilibration at 1000 K for 10 ns, cooling down from 1000 K to 300 K in 2 ns, and equilibration at 300K for 2 ns) to randomize the solute positions.  Calculations were performed with AMBER14/16.

We set the maximum temperature of REMD to 380 K at which sufficient exchange of molecules between assemblies was observed. The initial structures of each replicas were prepared in the same manner as for the conventional MD simulations. The number of the replicas was 40 each for VPAA1 and VPAA2, and the target temperatures were set to realize enough exchange between each replica as 300.00, 301.70, 303.41, 305.12, 306.85, 308.60, 310.37, 312.16, 313.97, 315.80, 317.65, 319.52, 321.41, 323.32, 325.25, 327.20, 329.17, 331.16, 333.17, 335.20, 337.25, 339.32, 341.41, 343.52, 345.65, 347.80, 349.97, 352.16, 354.37, 356.60, 358.85, 361.12, 363.41, 365.72, 368.05, 370.40, 372.77, 375.16, 377.57, and 380.00 K. The exchange attempts were performed at every 2 ps. Equilibrium simulations were performed for 1 µs in NPT ensemble. The average exchange probability was 20 %.