git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13464 f3b2605a-c512-4ea7-a41b-209d697bcdaa

examples/USER/fep/CH4hyd/fep01/fep01.lmp

@@ -1,22 +1,22 @@
-# Time-averaged data for fix fFEP
-# TimeStep c_cFEP[1] c_cFEP[2]
-125000 0.0806308 0.881044
-250000 0.251798 0.66945
-375000 0.448135 0.502774
-500000 0.670275 0.384034
-625000 0.873864 0.343148
-750000 0.689533 0.484145
-875000 0.474153 0.600305
-1000000 0.303566 0.740249
-1125000 0.165693 0.855143
-1250000 0.130949 0.88524
-1375000 0.0518948 0.976114
-1500000 0.0283335 1.0025
-1625000 -0.000790228 1.04259
-1750000 -0.0263791 1.0736
-1875000 -0.0587947 1.12568
-2000000 -0.0764999 1.15472
-2125000 -0.091264 1.17869
-2250000 -0.11294 1.21778
-2375000 -0.130721 1.25162
-2500000 -0.151808 1.29392
+# Time-averaged data for fix FEP
+# TimeStep c_FEP[1] c_FEP[2]
+100000 0.0735182 0.889583
+200000 0.241868 0.679931
+300000 0.407677 0.542008
+400000 0.709112 0.360902
+500000 0.718538 0.428553
+600000 0.639674 0.516854
+700000 0.482835 0.586307
+800000 0.289216 0.746055
+900000 0.192641 0.823932
+1000000 0.113029 0.908737
+1100000 0.0619301 0.96572
+1200000 0.0197356 1.01976
+1300000 0.00310596 1.03223
+1400000 -0.0300484 1.08295
+1500000 -0.0714914 1.14599
+1600000 -0.0712604 1.14573
+1700000 -0.109089 1.2123
+1800000 -0.117256 1.22671
+1900000 -0.132337 1.25534
+2000000 -0.153557 1.29745

examples/USER/fep/CH4hyd/fep01/in.fep01.lmp

@@ -30,51 +30,54 @@ pair_coeff    1    4  lj/cut/tip4p/long/soft   0.0000   1.0000  0.0  # C4H Hw
 pair_coeff    2    3  lj/cut/tip4p/long/soft   0.0699   2.8126  0.0  # H Ow
 pair_coeff    2    4  lj/cut/tip4p/long/soft   0.0000   1.0000  0.0  # H Hw
 
-variable nsteps equal 2500000
-variable nprint equal ${nsteps}/500
-variable ndump equal ${nsteps}/100
+variable TK equal 300.0
+variable PBAR equal 1.0
 
-variable temp equal 300.0
-variable press equal 1.0
-
-fix fSHAKE all shake 0.0001 20 ${nprint} b 2 a 2
+fix SHAKE all shake 0.0001 20 0 b 2 a 2
 
 neighbor 2.0 bin
 
-timestep 2.0
+timestep 1.0
 
-velocity all create ${temp} 12345
+velocity all create ${TK} 12345
 
 thermo_style multi
-thermo ${nprint}
+thermo 5000
 
-fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 1000
+fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000
 
-run 250000
+set type 1*2 charge 0.0
 
+run 100000
 reset_timestep 0
 
 variable lambda equal ramp(0.0,1.0)
+variable q1 equal -0.24*v_lambda
+variable q2 equal  0.06*v_lambda
 
-fix fADAPT all adapt/fep 125000 pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_lambda after yes
+fix ADAPT all adapt/fep 100000 &
+  pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_lambda &
+  atom charge 1 v_q1 &
+  atom charge 2 v_q2 &
+  after yes
+
+fix PRINT all print 100000 "adapt  lambda = ${lambda}  q1 = ${q1}  q2 = ${q2}"
 
 variable dlambda equal 0.05
+variable dq1 equal -0.24*v_dlambda
+variable dq2 equal  0.06*v_dlambda
 
-compute cFEP all fep ${temp} pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda
+compute FEP all fep ${TK} &
+  pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda &
+  atom charge 1 v_dq1 &
+  atom charge 2 v_dq2
 
-fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fep01.lmp
+fix FEP all ave/time 20 4000 100000 c_FEP[1] c_FEP[2] file fep01.lmp
 
-# compute cRDF all rdf 100 3 3 3 4 4 4
-# fix fRDF all ave/time 2000 500 ${nsteps} c_cRDF file rdf.lammps mode vector
+dump TRAJ all custom 20000 dump.lammpstrj id mol type element x y z ix iy iz
+dump_modify TRAJ element C H O H
 
-group owater type 3
-compute cMSD owater msd
-fix fMSD owater ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
-
-dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
-dump_modify dCONF element C H O H
-
-run ${nsteps}
+run 2000000
 
 # write_restart restart.*.lmp
 write_data data.*.lmp