MA-CA-SP molecular dynamics trajectory for HIV-1 Gag protein

MA-CA-SP1_trajectory.tar.gz is a compressed folder containing files md_0_1.gro and md_0_1.xtc that
correspond to a molecular dynamics trajectory of 50 ns for MA-CA-SP1. This model includes amino acids 2 to
377 of protein GAG-HIV1 (UNIPROT code P12497) in a compact
conformation.

md.mdp is a text file with the conditions to generate the molecular dynamics run.

The
simulation was performed using the GROMACS package version 2018.1
(Abraham et al., 2015) in conjunction with the GROMOS 53A6 force field (Oostenbrink et al., 2004). Water was represented
explicitly using the SPC/E model (Berendsen et al.,1987). The system
was simulated under periodic conditions in a dodecahedron box. The
temperature was maintained throughout the simulation by independently
coupling the protein and the solvent to an external temperature bath
at 310 K with a coupling constant tau_t= 0.1 ps using a modified
Berendsen thermostat (Bussi et al., 2007). The pressure was
maintained at 1 bar by weakly coupling the system to an isotropic
pressure bath (Parrinello & Rahman., 1981) using an isothermal
compressibility of 4.5 x 10-5

bar-1
and a coupling constant of tau_p= 2.0 ps. During the
simulations, the length of all bonds within the protein was
constrained using the LINear Constraint Solver (LINCS) algorithm
(Hess et al. 1997). All bonds, even heavy atom-H bonds were
constrained. The time step for integrating the equations of motion
was 2 fs. The algorithm used for computing long range electrostatic
interactions was Particle-Mesh-Ewald (PME) (Petersen et al. 1995).

Abraham,
M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B.,
Lindahl, E. (2015) SoftwareX 1–2:19–25.

Berendsen,
H. J. C., Postma, J. P .M., and van Gunsteren, W. F., DiNola, A.,
Haak, J. R. (1984). J. Chem. pHYS. 81, 3684-3690.

Bussi,
G., Donadio, D., Parrinello, M., (2007). J. Chem. Phys. 126,
014101-7.

Hess,
B., Bekker, H.,Berendsen, H.J.C., and Fraaijc, J. G.E.M. (1997). J.
Comput. Chem. 18, 1463-1472.

Oostenbrink
B.C., Pitera J.W., Lipzig M.M.H., Meerman J.H.N., Gunsteren W.F. van
(2000) J. Comput. Chem. 25:1656-1676.

Parrinello,
M. and Rahman, A. (1981). J. Appl. Phys. 52, 7182-7190.

Petersen
H. G. (1995) J. Chem. Phys. 103, 3668-3679.