bin/coords2coords bin/coulomb bin/dcd2dcd bin/iSGProtomol bin/protomol bin/xyzviz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/coulomb_309/309ca.config %%PORTEXAMPLES%%%%EXAMPLESDIR%%/coulomb_309/309ca.par %%PORTEXAMPLES%%%%EXAMPLESDIR%%/coulomb_309/309ca.pos.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/coulomb_309/309ca.psf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/alanine_dipeptide_water_184x/alanine.equil.psf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/alanine_dipeptide_water_184x/alanine.7ns.namd %%PORTEXAMPLES%%%%EXAMPLESDIR%%/alanine_dipeptide_water_184x/alanine.equil.pdb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/alanine_dipeptide_water_184x/ala607.pgn %%PORTEXAMPLES%%%%EXAMPLESDIR%%/alanine_dipeptide_water_184x/alanine.namd %%PORTEXAMPLES%%%%EXAMPLESDIR%%/alanine_dipeptide_water_184x/alanine.pdb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/alanine_dipeptide_water_184x/alanine.psf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/argon_400/argon.par %%PORTEXAMPLES%%%%EXAMPLESDIR%%/argon_400/argon.lf.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/argon_400/argon.npt.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/argon_400/argon.pdb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/argon_400/argon.psf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/argon_400/argon.vel.pdb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/bpti_water_1101/bpti.par %%PORTEXAMPLES%%%%EXAMPLESDIR%%/bpti_water_1101/bpti.hmc.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/bpti_water_1101/bpti.lf.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/bpti_water_1101/bpti.pdb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/bpti_water_1101/bpti.psf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/bpti_water_1101/bpti.shmc.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/bpti_water_14281/bpti.shake.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/bpti_water_14281/bpti.ewald.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/bpti_water_14281/bpti.mg.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/bpti_water_14281/bpti.namd %%PORTEXAMPLES%%%%EXAMPLESDIR%%/bpti_water_14281/bpti.par %%PORTEXAMPLES%%%%EXAMPLESDIR%%/bpti_water_14281/bpti.pbc.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/bpti_water_14281/bpti.pdb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/bpti_water_14281/bpti.psf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane_4/runButaneTests.sh %%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane_4/README %%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane_4/UA_butane.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane_4/UA_butane.dhmc.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane_4/UA_butane.hmc.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane_4/UA_butane.lf.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane_4/UA_butane.par %%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane_4/UA_butane.pdb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane_4/UA_butane.psf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane_4/angleSetDHMC %%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane_4/cleanOutput.bash %%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane_4/dihedralSetDHMC %%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane_4/procDihedralFile.awk %%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane_4/runButaneResults.sh %%PORTEXAMPLES%%%%EXAMPLESDIR%%/alanine_dipeptide_23/ala_equil.pdb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/alanine_dipeptide_23/ala_equil.psf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/alanine_dipeptide_23/ala_equilibrated.pdb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/alanine_dipeptide_23/ala_equilibrated.pgn %%PORTEXAMPLES%%%%EXAMPLESDIR%%/decalanine_66/dihedralIndexSet %%PORTEXAMPLES%%%%EXAMPLESDIR%%/decalanine_66/alanine.BSplineMOLLY.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/decalanine_66/alanine.Equilibrium.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/decalanine_66/alanine.LF.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/decalanine_66/alanine.LFwDihedralOut.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/decalanine_66/alanine.PLF.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/decalanine_66/alanine.Shake.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/decalanine_66/alanine.par %%PORTEXAMPLES%%%%EXAMPLESDIR%%/decalanine_66/alanine.pdb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/decalanine_66/alanine.psf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/decalanine_66/alanine.testSet %%PORTEXAMPLES%%%%EXAMPLESDIR%%/decalanine_66/alanine.water.pdb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/decalanine_66/alanine.water.psf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/electrons_22/22el.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/electrons_22/22el.pos.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/electrons_22/22el.psf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/electrons_22/22el.vel.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/electrons_22/el.par %%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane_ethane_xxx/iSGMD_README %%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane.par %%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane.trans %%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane_100.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane_100_Pure_Trappe.coor.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane_100_Pure_Trappe.psf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane_100_Pure_Trappe.vel.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane_100_Pure_Trappe.xsc %%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane_300.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane_300_Pure_Trappe.coor.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane_300_Pure_Trappe.psf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane_300_Pure_Trappe.vel.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane_300_Pure_Trappe.xsc %%PORTEXAMPLES%%%%EXAMPLESDIR%%/testset/test.tcsh %%PORTEXAMPLES%%%%EXAMPLESDIR%%/testset/README %%PORTEXAMPLES%%%%EXAMPLESDIR%%/testset/hmc.Bsp_PME.pb.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/testset/hmc.std.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/testset/lf.Ewald.pb.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/testset/lf.MG.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/testset/lf.PME.pb.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/testset/lf.std.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/testset/lf.std.pb.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/testset/shmc.Bsp_PME.pb.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/testset/shmc.std.pb.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/testset/slf.std.pb.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_216/water216.vel.pdb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_216/water216.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_216/water216.coor.pdb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_216/water216.new.pos.pdb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_216/water216.new.vel.pdb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_216/water216.par %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_216/water216.psf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_648/water648.tip3.psf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_648/water648.fluid.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_648/water648.fluid.pos.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_648/water648.ice.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_648/water648.ice.nvt.conf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_648/water648.ice.pos.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_648/water648.spce.par %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_648/water648.spce.psf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_648/water648.tip3.par %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/coulomb_309 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/alanine_dipeptide_water_184x %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/argon_400 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/bpti_water_1101 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/bpti_water_14281 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/butane_4 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/alanine_dipeptide_23 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/decalanine_66 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/electrons_22 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/methane_ethane_xxx %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/testset %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/water_216 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/water_648 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%