We present here all the necessary files to run the simulations in the same way as described in the main text for the 
system with 200 POPC lipid molecules with 75 waters/lipid with 4 [Gd(DOTA)]- and with 4 Na+. All files are in GROMACS 
format. In the folder ./simulation_files we have all the necessary files to run the simulation that includes force fields
and parameters to run the simulation (*.mdp). In the folder ./coordinate_files we have the initial coordinates of 
the systems for all the replicates performed in this work after a minimization step to remove any bad contact 
(*-after_minimization.gro). In this folder we also give the final coordinates of each of these replicates
(*_last_frame.gro). Full trajectories are available upon request.

The Slipids force field folder were obtain from http://www.fos.su.se/~sasha/SLipids/Downloads.html, accessed in 2019, 
corresponding to the data published in:

	Jämbeck, J. P. M.; Lyubartsev, A. P. An Extension and Further Validation of an All-Atomistic Force Field for 
	Biological Membranes. J. Chem. Theory Comput. 2012, 8 (8), 2938–2948. https://doi.org/10.1021/ct300342n.

	Jämbeck, J. P. M.; Lyubartsev, A. P. Derivation and Systematic Validation of a Refined All-Atom Force Field for 
	Phosphatidylcholine Lipids. J. Phys. Chem. B 2012, 116 (10), 3164–3179. https://doi.org/10.1021/jp212503e.

	Several bonded and nonbonded parameters used to parametrize the Slipids force field 
	come from CHARMM36:

	Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias,
	Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr. and Richard W. Pastor "Update of
	the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types" 
	J. Phys. Chem. B, 2010, 114 (23), pp 7830–7843. https://doi.org/10.1021/jp101759q

The parametrization of the contrast agent [Gd(DOTA)]- was done by us and published under the license CC-BY 4.0 in:

	Oliveira, A. C.; Filipe, H. A. L.; Ramalho, J. P. P.; Salvador, A.; Geraldes, C. F. G. C.; Moreno, M. J.; 
	Loura, L. M. S. Modeling Gd3+ Complexes for Molecular Dynamics Simulations: Toward a Rational Optimization of
	MRI Contrast Agents. Inorg. Chem. 2022, 61 (30), 11837–11858. https://doi.org/10.1021/acs.inorgchem.2c01597.

	This parametrization of [Gd(DOTA)]- were done by using some of the parameters from General Amber Force Field:
	
	Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and Testing of a General
	Amber Force Field. J. Comput. Chem. 2004, 25 (9), 1157–1174. https://doi.org/10.1002/jcc.20035.

the original TIP3P water model was used with the Lennard-Jones parameters for the hydrogens atoms set to zero:

	Jorgensen, W. L. Quantum and Statistical Mechanical Studies of Liquids. 10. Transferable Intermolecular
	Potential Functions for Water, Alcohols, and Ethers. Application to Liquid Water. 
	J. Am. Chem. Soc. 1981, 103 (2), 335–340. https://doi.org/10.1021/ja00392a016.
	
	Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential
	Functions for Simulating Liquid Water. J. Chem. Phys. 1983, 79 (2), 926–935. https://doi.org/10.1063/1.445869.

Sodium ion parameters were also obtained from the Slipids force field webpage. These parameters come form amber
force fields such as GAFF:
	Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and Testing of a General
	Amber Force Field. J. Comput. Chem. 2004, 25 (9), 1157–1174. https://doi.org/10.1002/jcc.20035.


generic simulation commands:
gmx grompp -f minimization.mdp -c water_replica1_after_minimization.gro -p topol.top -o minimization.tpr >& minimization_grompp.job ;
gmx mdrun -v -deffnm minimization >& minimization_mdrun.job ;
gmx grompp -f NVT.mdp -c minimization.gro -p topol.top -n index.ndx -o equilibration_NVT.tpr >& equilibration_NVT_grompp.job ;
gmx mdrun -v -deffnm equilibration_NVT >& equilibration_NVT_mdrun.job ;
gmx grompp -f NPT.mdp -c equilibration_NVT.gro -t equilibration_NVT.cpt -p topol.top -n index.ndx -o equilibration_NPT.tpr >& equilibration_NPT_grompp.job ; 
gmx mdrun -v -deffnm equilibration_NPT >& equilibration_NPT_mdrun.job ;
gmx grompp -f mdrun.mdp -c equilibration_NPT.gro -t equilibration_NPT.cpt -p topol.top -n index.ndx -o mdrun_trajectory.tpr >& mdrun_trajectory_grompp.job ;
gmx mdrun -v -deffnm mdrun_trajectory >& mdrun_trajectory.job ;


For any question, fell free to contact us at:
	ac_oliveira10@hotmail.com or mmoreno@ci.uc.pt or lloura@ff.uc.pt


