DOI: 10.5281/zenodo.13772542
title: Simulation trajectories for the article "Simulated Solute Tempering 2"

description: Simulation trajectories for the article "Simulated Solute Tempering 2".

For each set of simulation is provided:



One .pdb file of the system without solvant and hydrogen atoms coordinates.

Trajectorie files in .xtc format without solvant and hydrogen atoms coordinates for each of the 4 replicas.

DataFrame files in .csv format containing:



Aim Temp (K)

E solute scaled (kJ/mole)

E solute not scaled (kJ/mole)

E solvent (kJ/mole)

E solvent-solute (kJ/mole)

Step

Potential Energy (kJ/mole)

Total Energy (kJ/mole)

Temperature (K)

Speed (ns/day)

Time(µs)

lambda




List of files:

.
├── CLN025
│  ├── SST2
│  │   ├── CLN025_SST2_F_1.csv
│  │   ├── CLN025_SST2_F_1.pdb
│  │   ├── CLN025_SST2_F_1.xtc
│  │   ├── CLN025_SST2_F_2.csv
│  │   ├── CLN025_SST2_F_2.xtc
│  │   ├── CLN025_SST2_F_3.csv
│  │   ├── CLN025_SST2_F_3.xtc
│  │   ├── CLN025_SST2_F_4.csv
│  │   ├── CLN025_SST2_F_4.xtc
│  │   ├── CLN025_SST2_F_6_rungs_1.csv
│  │   ├── CLN025_SST2_F_6_rungs_1.xtc
│  │   ├── CLN025_SST2_F_6_rungs_2.csv
│  │   ├── CLN025_SST2_F_6_rungs_2.xtc
│  │   ├── CLN025_SST2_F_6_rungs_3.csv
│  │   ├── CLN025_SST2_F_6_rungs_3.xtc
│  │   ├── CLN025_SST2_F_6_rungs_4.csv
│  │   ├── CLN025_SST2_F_6_rungs_4.xtc
│  │   ├── CLN025_SST2_F_6_rungs.pdb
│  │   ├── CLN025_SST2_F_Tref_350_1.csv
│  │   ├── CLN025_SST2_F_Tref_350_1.pdb
│  │   ├── CLN025_SST2_F_Tref_350_1.xtc
│  │   ├── CLN025_SST2_F_Tref_350_2.csv
│  │   ├── CLN025_SST2_F_Tref_350_2.xtc
│  │   ├── CLN025_SST2_F_Tref_350_3.csv
│  │   ├── CLN025_SST2_F_Tref_350_3.xtc
│  │   ├── CLN025_SST2_F_Tref_350_4.csv
│  │   ├── CLN025_SST2_F_Tref_350_4.xtc
│  │   ├── CLN025_SST2_U_1.csv
│  │   ├── CLN025_SST2_U_1.pdb
│  │   ├── CLN025_SST2_U_1.xtc
│  │   ├── CLN025_SST2_U_2.csv
│  │   ├── CLN025_SST2_U_2.xtc
│  │   ├── CLN025_SST2_U_3.csv
│  │   ├── CLN025_SST2_U_3.xtc
│  │   ├── CLN025_SST2_U_4.csv
│  │   └── CLN025_SST2_U_4.xtc
│  └── ST
│      ├── CLN025_ST_F_1.csv
│      ├── CLN025_ST_F_1.xtc
│      ├── CLN025_ST_F_2.csv
│      ├── CLN025_ST_F_2.xtc
│      ├── CLN025_ST_F_3.csv
│      ├── CLN025_ST_F_3.xtc
│      ├── CLN025_ST_F_4.csv
│      ├── CLN025_ST_F_4.xtc
│      ├── CLN025_ST_F.pdb
│      ├── CLN025_ST_U_1.csv
│      ├── CLN025_ST_U_1.xtc
│      ├── CLN025_ST_U_2.csv
│      ├── CLN025_ST_U_2.xtc
│      ├── CLN025_ST_U_3.csv
│      ├── CLN025_ST_U_3.xtc
│      ├── CLN025_ST_U_4.csv
│      ├── CLN025_ST_U_4.xtc
│      └── CLN025_ST_U.pdb
├── PNGase_p97
│  ├── PNGase_p97_F_1.csv
│  ├── PNGase_p97_F_1.xtc
│  ├── PNGase_p97_F_2.csv
│  ├── PNGase_p97_F_2.xtc
│  ├── PNGase_p97_F_3.csv
│  ├── PNGase_p97_F_3.xtc
│  ├── PNGase_p97_F_4.csv
│  ├── PNGase_p97_F_4.xtc
│  ├── PNGase_p97_F.pdb
│  ├── PNGase_p97_U_1.csv
│  ├── PNGase_p97_U_1.xtc
│  ├── PNGase_p97_U_2.csv
│  ├── PNGase_p97_U_2.xtc
│  ├── PNGase_p97_U_3.csv
│  ├── PNGase_p97_U_3.xtc
│  ├── PNGase_p97_U_4.csv
│  ├── PNGase_p97_U_4.xtc
│  └── PNGase_p97_U.pdb
└── TrpCage
    ├── SST2
    │   ├── TrpCage_SST2_F_1.csv
    │   ├── TrpCage_SST2_F_1.pdb
    │   ├── TrpCage_SST2_F_1.xtc
    │   ├── TrpCage_SST2_F_2.csv
    │   ├── TrpCage_SST2_F_2.xtc
    │   ├── TrpCage_SST2_F_3.csv
    │   ├── TrpCage_SST2_F_3.xtc
    │   ├── TrpCage_SST2_F_4.csv
    │   ├── TrpCage_SST2_F_4.xtc
    │   ├── TrpCage_SST2_F_Tref_350_1.csv
    │   ├── TrpCage_SST2_F_Tref_350_1.pdb
    │   ├── TrpCage_SST2_F_Tref_350_1.xtc
    │   ├── TrpCage_SST2_F_Tref_350_2.csv
    │   ├── TrpCage_SST2_F_Tref_350_2.xtc
    │   ├── TrpCage_SST2_F_Tref_350_3.csv
    │   ├── TrpCage_SST2_F_Tref_350_3.xtc
    │   ├── TrpCage_SST2_F_Tref_350_4.csv
    │   ├── TrpCage_SST2_F_Tref_350_4.xtc
    │   ├── TrpCage_SST2_U_1.csv
    │   ├── TrpCage_SST2_U_1.pdb
    │   ├── TrpCage_SST2_U_1.xtc
    │   ├── TrpCage_SST2_U_2.csv
    │   ├── TrpCage_SST2_U_2.xtc
    │   ├── TrpCage_SST2_U_3.csv
    │   ├── TrpCage_SST2_U_3.xtc
    │   ├── TrpCage_SST2_U_4.csv
    │   └── TrpCage_SST2_U_4.xtc
    └── ST
        ├── TrpCage_ST_F_1.csv
        ├── TrpCage_ST_F_1.xtc
        ├── TrpCage_ST_F_2.csv
        ├── TrpCage_ST_F_2.xtc
        ├── TrpCage_ST_F_3.csv
        ├── TrpCage_ST_F_3.xtc
        ├── TrpCage_ST_F_4.csv
        ├── TrpCage_ST_F_4.xtc
        ├── TrpCage_ST_F.pdb
        ├── TrpCage_ST_U_1.csv
        ├── TrpCage_ST_U_1.xtc
        ├── TrpCage_ST_U_2.csv
        ├── TrpCage_ST_U_2.xtc
        ├── TrpCage_ST_U_3.csv
        ├── TrpCage_ST_U_3.xtc
        ├── TrpCage_ST_U_4.csv
        ├── TrpCage_ST_U_4.xtc
        └── TrpCage_ST_U.pdb