MxMD Simulation Details

System Setup

By default, ten cosolvent/water systems are generated for each probe. Each system contains the input structure of the protein or DNA/RNA target (solute), a 7 Å layer of organic cosolvent and water molecules. The number of cosolvent molecules is tuned to be approximately 5% volume by volume.

The default procedure to generate the cosolvent/water mixture is as follows:

1. Solvate the input solute structure with the cosolvent system.

2. Remove all cosolvent molecules that overlap with the solute, or that are farther than 7 Å away from the solute.

   The overlap is determined by scaling the van der Waals radius of the probe by the factor s_vdw:

   

   where is the number of heavy atoms in the probe. Thus, larger probes have a greater scaling factor.

3. Solvate the solute/cosolvent system in water with a solvent buffer of 15 Å.

4. Shrink the size of the water box to match the target ratio of cosolvent to water (5% volume by volume).

   

   where N_wat and N_probes are the number of water and probe molecules; m_wat and m_probe are the masses of one water and probe molecule; vv_target is the target volume by volume (v/v) ratio; and ρ_probe is the density of the probe’s homogeneous mixture at 300 K.

System Setup for Membrane Proteins

The procedure to generate the cosolvent/water mixture for a membrane protein is as follows:

1. Solvate the input protein structure with the cosolvent system.

2. Place the membrane bilayer and waters around the protein.

3. Remove all cosolvent molecules that overlap with the protein.

   The overlap is determined by scaling the van der Waals radius of the probe by the factor s_vdw:

   

   where is the number of heavy atoms in the probe. Thus, larger probes have a greater scaling factor.

   Cosolvent molecules that are farther than 7 Å away from the membrane or protein are also removed.

4. Remove all the cosolvent molecules that overlap with the lipids.

5. Remove all the waters that overlap with the cosolvent molecules.

6. Shrink the size of the water/lipid box to match the target ratio of cosolvent to water (5% volume by volume).

   

   where N_wat and N_probes are the number of water and probe molecules; m_wat and m_probe are the masses of one water and probe molecule; vv_target is the target volume by volume (v/v) ratio; and ρ_probe is the density of the probe’s homogeneous mixture at 300 K.

MxMD Simulation Protocol

The cumulative simulation time for each cosolvent/water system is approximately 20 ns by default. The first 15 ns are used for equilibrating the system. The last 5 ns are used for data collection. The simulation protocol consists of the following stages:

1. 24 ps Brownian Dynamics, NVT, T = 10 K, timestep = 1 fs, restraints on all solute atoms
2. 24 ps Brownian Dynamics (MD), NVT, T = 10 K, timestep = 1 fs, restraints on solute heavy atoms
3. 12 ps MD, NVT, T = 10 K, timestep = 1 fs, restraints on solute heavy atoms
4. 12 ps MD, NPT, T = 10 K, p = 1.013 bar, timestep = 2 fs, restraints on solute heavy atoms
5. 12 ps MD, NPT, T = 300 K, p = 1.013 bar, timestep = 2 fs, restrains on solute heavy atoms
6. 15 ns MD, NPT, T = 300 K, p = 1.013 bar, timestep = 2 fs, no restraints
7. 5 ns MD, NPT, T = 300 K, p = 1.013 bar, timestep = 2 fs, no restraints

The last stage is used to collect data. A trajectory frame is written every 4.8 ps, corresponding to approximately 1000 trajectory frames per cosolvent/water simulation for the default simulation time. The trajectory is written in XTC format. See Trajectory Player for more information.