improved figures

Author: simongravelle

figures/PEG-density.png

@@ -34,7 +34,7 @@ compute dphi PEG dihedral/local phi
 thermo_style custom step temp etotal c_rgyr # c_mphi
 thermo 250
 
-dump mydmp all local 100 pull.dat index c_dphi c_prop
+dump mydmp all local 50 pull.dat index c_dphi c_prop
 
 # S.G.: a histogram would be ok if one could select only dihedral 2 
 # fix myhisto all ave/histo 100 120 15000 0 180 90 c_dphi file pull.dat ave running mode vector

figures/PEG-distance.png

@@ -37,12 +37,15 @@ dump_modify viz backcolor white &
 
 variable myvol equal vol
 variable myoxy equal count(H2O)/3
-variable rho equal ${myoxy}/v_myvol
+variable NA equal 6.022e23
+variable Atom equal 1e-10
+variable M equal 0.018015
+variable rho equal ${myoxy}*${M}/(v_myvol*${NA}*${Atom}^3)
 thermo 500
 thermo_style custom step temp etotal v_myvol v_rho
 
 timestep 1.0
-run 10000
+run 15000
 
 write_restart water.restart
 # write_data water.data # uncomment to write a .data file as well