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

examples/USER/fep/CH4hyd/fep10/fep10.lmp

@@ -1,22 +1,22 @@
-# Time-averaged data for fix fFEP
-# TimeStep c_cFEP[1] c_cFEP[2]
-125000 0.156203 0.771285
-250000 0.136448 0.799233
-375000 0.12198 0.820426
-500000 0.109453 0.840255
-625000 0.0921141 0.868102
-750000 0.0713015 0.905735
-875000 0.0622431 0.922352
-1000000 0.0330546 0.981942
-1125000 0.0197866 1.01134
-1250000 -0.00412826 1.06765
-1375000 -0.0174302 1.11343
-1500000 -0.0511646 1.18453
-1625000 -0.105676 1.36325
-1750000 -0.161616 1.56478
-1875000 -0.258263 1.93825
-2000000 -0.447487 3.0595
-2125000 -0.549377 3.01163
-2250000 -0.379009 2.01933
-2375000 -0.20934 1.45678
-2500000 -0.0644056 1.1252
+# Time-averaged data for fix FEP
+# TimeStep c_FEP[1] c_FEP[2]
+100000 0.160455 0.766272
+200000 0.141912 0.791902
+300000 0.119585 0.824744
+400000 0.104694 0.847809
+500000 0.0917124 0.869318
+600000 0.0859541 0.881974
+700000 0.0666319 0.920268
+800000 0.0428654 0.965893
+900000 0.0240106 0.999889
+1000000 0.0294147 0.997671
+1100000 -0.0214947 1.11583
+1200000 -0.0543642 1.23078
+1300000 -0.0665772 1.25986
+1400000 -0.196675 1.66521
+1500000 -0.341037 2.39926
+1600000 -0.480217 2.97287
+1700000 -0.405599 2.36311
+1800000 -0.415165 2.12414
+1900000 -0.229669 1.49644
+2000000 -0.0838847 1.15743

examples/USER/fep/CH4hyd/fep10/in.fep10.lmp

@@ -30,51 +30,53 @@ pair_coeff    1    4  lj/cut/tip4p/long/soft   0.0000   1.0000  1.0  # C4H Hw
 pair_coeff    2    3  lj/cut/tip4p/long/soft   0.0699   2.8126  1.0  # H Ow
 pair_coeff    2    4  lj/cut/tip4p/long/soft   0.0000   1.0000  1.0  # 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
+run 100000
 
 reset_timestep 0
 
 variable lambda equal ramp(1.0,0.0)
+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 fep10.lmp
+fix FEP all ave/time 20 4000 100000 c_FEP[1] c_FEP[2] file fep10.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