virus.in
775e8f3cc8f5lammm-master-deprecated

virus.in
View Options

			# Simple virus model.
			#

			units lj
			dimension 3
			boundary f f f

			atom_style angle
			pair_style lj/cut 4.0
			pair_modify shift yes
			bond_style harmonic
			angle_style harmonic

			neigh_modify binsize 5.0

			read_data init.data

			group NC type 1
			group rest type 2 3 4
			group CA type 3


			timestep 0.0001
			variable R equal "ramp(v_R0,v_R1)"

			variable RF equal ${R1}
			variable Rw equal "v_RF - 0.5"

			print "** R scales from ${R0} to ${R1} and wall is at ${Rw} **"

			variable rr atom "sqrt( xx + yy + z*z )"
			compute ravg CA reduce ave v_rr

			region my_sphere sphere 0 0 0 v_Rw side out
			fix wall all wall/region my_sphere lj126 1.0 1.0 1.1225


			variable U equal pe
			variable epair equal epair
			fix U all ave/time 2000 1 2000 v_U v_R v_epair
			variable t equal time
			variable ravg equal c_ravg

			variable T equal 0.25

			variable pU equal f_U[1]
			variable pE equal f_U[3]

			fix out all print 2000 "$t ${pU} $R ${ravg} ${pE}" file thermo.${DATA}.dat screen no

			fix step1 rest nvt temp $T $T 1.0
			fix step2 NC nvt/manifold/rattle 1e-4 10 sphere v_R temp $T $T 1.0

			special_bonds lj 0 0 0

			angle_coeff 1 250.0 180.0

			thermo_style custom time step pe v_pU ke etotal epair temp v_R
			thermo 10000



			compute pe all pe/atom
			fix pe_avg all ave/atom 100 50 5000 c_pe


			dump traj_all all custom 5000 virus.dump id type x y z f_pe_avg

			run 2500000
			unfix out

			fix step1 rest nvt temp $T $T 1.0
			fix step2 NC nvt/manifold/rattle 1e-4 10 sphere ${R1} temp $T $T 1.0

			run 1000000