Thread: [apbs-users] Sensitivity of total electrostatic energy to dime
Biomolecular electrostatics software
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From: MikeK <mik...@gm...> - 2012-04-05 11:37:15
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READ mol pqr mike.pqr END ELEC name mike-elec mg-auto # multigrid sequential focussing PB dime 193 161 161 # grid dimensions cglen 85.6 77.9 79.0 # coarse grain lengths fglen 71.6 63.9 65.0 cgcent mol 1 # coarse grid centered on molecule 1 fgcent mol 1 # fine grid centered on molecule 1 mol 1 npbe bcfl sdh # multiple Debye-Huckel BC pdie 2 # solute dielectric ion charge 1 conc 0.15 radius 2.0 # 150 mM Na+ ion charge -1 conc 0.15 radius 2.0 # 150 mM Cl- sdie 78 # solvent dielectric srfm mol # traditional molecular surface chgm spl2 # cubic B-spline charge mapping sdens 10.0 # sphere density srad 1.4 # solvent probe radius swin 0.3 # temp 300.0 # temperature calcenergy total calcforce no END APOLAR name mike-apol bconc 0.0 # eliminate integral term gamma 0.2 # surface tension coefficient in kJ/mol/Ang2 press 0.0 # solvent pressure zero to eliminate volume term grid 0.25 0.25 0.25 # grid spacing for volume integrals swin 0.3 # size of support srad 1.4 # solvent radius srfm sacc # surface model = solvent accessible surface sdens 20 # no of points/Ang2 dpos 0.75 # finite diff displacement for SA derivative calcs temp 300.0 # temperature mol 1 calcenergy total calcforce no END print elecEnergy mike-elec end print apolEnergy mike-apol end QUIT |