diff --git a/puremd_rc_1003/environ/param.gpu.water b/puremd_rc_1003/environ/param.gpu.water index 53669d3fe6c0c1219e8b6e863f14c3b9ca1dd282..1a9cd60f8d281dfdac0fe0e906af5cedaec42237 100644 --- a/puremd_rc_1003/environ/param.gpu.water +++ b/puremd_rc_1003/environ/param.gpu.water @@ -1,7 +1,7 @@ simulation_name water.6.notab ! output files will carry this name + their specific extension ensemble_type 0 ! 0: NVE, 1: NVT, 2: anisotropic NPT, 3: semi-isotropic NPT, 4: isotropic NPT 6: berendsen NVT -nsteps 10 ! number of simulation steps -dt 0.1 ! time step in fs +nsteps 100 ! number of simulation steps +dt 0.25 ! time step in fs reposition_atoms 0 ! 0: just fit to periodic boundaries, 1: CoM to the center of box, 3: CoM to the origin restrict_bonds 0 ! enforce the bonds given in CONECT lines of pdb file for this many steps @@ -13,7 +13,9 @@ nbrhood_cutoff 5.0 ! near neighbors cutoff for bond calculations in A bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs thb_cutoff 0.001 ! cutoff value for three body interactions hbond_cutoff 7.50 ! cutoff distance for hydrogen bond interactions -q_err 1e-10 ! relative residual norm threshold used in GMRES +q_err 1e-6 ! relative residual norm threshold used in GMRES +ilu_refactor 100 ! nsteps to recompute incomplete LU factorization +ilu_droptol 0.3 ! threshold tolerance for dropping values in ILU temp_init 0.0 ! desired initial temperature of the simulated system temp_final 300.0 ! desired final temperature of the simulated system