fep CH4hyd examples

examples/USER/fep/CH4hyd/fdti10/in.fdti10.lmp

@@ -80,6 +80,8 @@ run 2000000
 
 unfix ADAPT
 
+# we don't want to evaluate the forward difference on the last point (lambda < 0)
+# so we simulate at 0.002 and perturb to 0.0
 variable lambda equal 0.002
 pair_coeff    1    3  lj/cut/tip4p/long/soft   0.1036   3.3279  ${lambda}  # C4H Ow
 pair_coeff    1    4  lj/cut/tip4p/long/soft   0.0000   1.0000  ${lambda}  # C4H Hw

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

@@ -0,0 +1,22 @@
+# Time-averaged data for fix FEP
+# TimeStep c_FEP[1] c_FEP[2]
+100000 0.0861965 0.869702
+200000 0.270598 0.646009
+300000 0.429399 0.513908
+400000 0.647082 0.389737
+500000 0.848196 0.337273
+600000 0.982763 0.356653
+700000 0.475609 0.599136
+800000 0.30114 0.74076
+900000 0.210652 0.802572
+1000000 0.0847226 0.941626
+1100000 0.0806783 0.943101
+1200000 0.00877851 1.03149
+1300000 -0.00283673 1.04327
+1400000 -0.0392469 1.0985
+1500000 -0.0544181 1.12144
+1600000 -0.083926 1.16893
+1700000 -0.0927886 1.1812
+1800000 -0.112133 1.21755
+1900000 -0.13743 1.26516
+2000000 -0.152623 1.29572

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

@@ -1,22 +0,0 @@
-# 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

@@ -72,7 +72,7 @@ compute FEP all fep ${TK} &
   atom charge 1 v_dq1 &
   atom charge 2 v_dq2
 
-fix FEP all ave/time 20 4000 100000 c_FEP[1] c_FEP[2] file fep01.lmp
+fix FEP all ave/time 20 4000 100000 c_FEP[1] c_FEP[2] file fep01.fep
 
 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

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

@@ -0,0 +1,22 @@
+# Time-averaged data for fix FEP
+# TimeStep c_FEP[1] c_FEP[2]
+100000 0.164483 0.761032
+200000 0.144176 0.78868
+300000 0.121538 0.821346
+400000 0.110912 0.839373
+500000 0.0877711 0.878701
+600000 0.0772824 0.894786
+700000 0.0599042 0.925429
+800000 0.0482336 0.952282
+900000 0.0235244 1.01104
+1000000 0.00669003 1.04034
+1100000 -0.0480557 1.23998
+1200000 -0.0394403 1.18336
+1300000 -0.183572 1.60602
+1400000 -0.18772 1.65213
+1500000 -0.288544 2.10261
+1600000 -0.407147 2.74905
+1700000 -0.426655 2.4725
+1800000 -0.444789 2.2147
+1900000 -0.209718 1.45201
+2000000 -0.0696584 1.13166

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

@@ -1,22 +0,0 @@
-# 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

@@ -71,7 +71,7 @@ compute FEP all fep ${TK} &
   atom charge 1 v_dq1 &
   atom charge 2 v_dq2
 
-fix FEP all ave/time 20 4000 100000 c_FEP[1] c_FEP[2] file fep10.lmp
+fix FEP all ave/time 20 4000 100000 c_FEP[1] c_FEP[2] file fep10.fep
 
 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