update examples for USER-FEP

examples/USER/fep/CC-CO/README.md

@@ -0,0 +1,87 @@
+Ethane to Methanol in Water
+===========================
+
+Example calculation of the difference in free energy of hydration upon
+transforming ethane into methanol with LAMMPS using *compute fep* and
+*fix adapt*.
+
+Ethane and methanol are represented by the OPLS-AA force field (1
+molecule). Water is represented by the 3-site SPC/E model (360
+molecules).
+
+The strategy used to perform the alchemical transformation is the
+following:
+
+* The dual topology approach is used, therefore all the atoms of
+  ethane and methanol are present throughout the simulation, only some
+  of them are dummy sites at the endpoints of the
+  transformation. Masses and intramolecular terms (bond lengths,
+  angles, dihedrals) are not changed.
+
+* Interactions of sites that are being created (from dummy sites) or
+  deleted (to become dummy sites) are treated using soft-core verions
+  of the Lennard-Jones and Coulomb potentials (*pair
+  lj/cut/coul/long/soft*) in order to avoid singularities. The
+  exponent of the coupling parameter lambda in the soft-core pair
+  potentials was in this example n = 1.
+
+* Eletrostatic charges that are modified are varied linearly from the
+  initial to the final values. This keeps the overall charge of the
+  molecule constant, which is good for the long range electrostatics
+  (the coupling parameter lambda has no effect on the kspace terms).
+
+The following directories contain input files and results for
+calculations using free-energy perturbation (FEP), thermodynamic
+integration (TI/FDTI) and Bennet's acceptance ratio methods:
+
+* `mols` -- Molcule description files and force field database used to
+  create the initial configurations for the simulations `data.0.lmp`
+  and `data.1.lmp`
+
+* `fep01` -- Calculation using FEP, multi-stage transformation of an
+  ethane molecule into methanol. Results in `fep01.lmp`
+
+* `fep10` -- Calculation using FEP, multi-stage transformation of a
+  methanol molecule into ethane. Results in `fep10.lmp`
+
+* `fdti01` -- Calculation using FDTI, transformation of an
+  ethane molecule into methanol. Results in `fdti01.lmp`
+
+* `fdti10` -- Calculation using FDTI, transformation of a
+  methanol molecule into ethane. Results in `fdti10.lmp`
+
+* `bar01` -- Calculation using BAR, 1-step transformation of an
+  ethane molecule into methanol. Results in `bar01.lmp`
+
+* `bar10` -- Calculation using BAR, 1-step transformation of a
+  methanol molecule into ethane. Results in `bar10.lmp`
+
+The free-energy profiles can be observed by plotting the values in the
+third column of the results files. The Python scripts `fep.py`,
+`nti.py`, `fdti.py`, and `bar.py` found in the `tools` directory can
+be used to calculate the free-energy differences corresponding to the
+above transformations:
+
+    fep.py 300 < fep01.lmp
+
+    fep.py 300 < fep10.lmp
+
+    nti.py 300 0.002 < fdti01.lmp
+
+    nti.py 300 0.002 < fdti10.lmp
+
+    fdti.py 300 0.002 < fdti01.lmp
+
+    fdti.py 300 0.002 < fdti10.lmp
+
+    bar.py 300 bar01.lmp bar10.lmp
+
+The outputs are in kcal/mol and can be compared with the experimental
+value of -6.93 kcal/mol and with simulation value from the literature:
+-6.7 kcal/mol [Jorgensen, Ravimohan, J Chem Phys 83 (1985) 3050], -6.8
+kcal/mol [Goette, Grubmüller, J Comp Chem 30 (2007) 447].
+
+These example calculations are for tutorial purposes only. The results
+may not be of research quality (not enough sampling, size of the step
+in lambda or of the delta for numerical derivative not optimized, no
+evaluation of ideal-gas contributions, etc.)

examples/USER/fep/CC-CO/fdti01/fdti01.lmp

@@ -1,22 +1,22 @@
 # Time-averaged data for fix fFEP
 # TimeStep c_cFEP[1] c_cFEP[2]
-125000 0.00863388 0.985635
-250000 0.00728772 0.987864
-375000 0.00567381 0.990544
-500000 0.00453181 0.992443
-625000 0.00329363 0.994511
-750000 0.00174226 0.997108
-875000 0.000549929 0.99911
-1000000 -0.00100228 1.00172
-1125000 -0.00220699 1.00375
-1250000 -0.00405928 1.00689
-1375000 -0.0059394 1.01009
-1500000 -0.0077451 1.01316
-1625000 -0.00999946 1.01701
-1750000 -0.0120579 1.02054
-1875000 -0.0148385 1.02533
-2000000 -0.0176808 1.03028
-2125000 -0.0256289 1.04418
-2250000 -0.0354112 1.06157
-2375000 -0.0445017 1.0779
-2500000 -0.0561655 1.09921
+125000 0.00871763 0.985497
+250000 0.00705519 0.98825
+375000 0.00568771 0.99052
+500000 0.00429336 0.992842
+625000 0.00308675 0.994856
+750000 0.00169928 0.997181
+875000 0.000144366 0.999789
+1000000 -0.00112539 1.00193
+1125000 -0.0026842 1.00456
+1250000 -0.00474318 1.00805
+1375000 -0.00571651 1.0097
+1500000 -0.0073978 1.01256
+1625000 -0.00966334 1.01644
+1750000 -0.011584 1.01972
+1875000 -0.0148498 1.02535
+2000000 -0.0192874 1.03307
+2125000 -0.0257123 1.04433
+2250000 -0.035944 1.06249
+2375000 -0.046465 1.08144
+2500000 -0.0558595 1.09863

examples/USER/fep/CC-CO/fdti01/in.fdti01.lmp

@@ -67,7 +67,7 @@ neighbor 2.0 bin
 
 timestep 2.0
 
-# velocity all create ${temp} 12345
+velocity all create ${temp} 12345
 
 thermo_style multi
 thermo ${nprint}

examples/USER/fep/CC-CO/fdti10/fdti10.lmp

@@ -1,22 +1,22 @@
 # Time-averaged data for fix fFEP
 # TimeStep c_cFEP[1] c_cFEP[2]
-125000 0.0627079 0.900432
-250000 0.0574303 0.908483
-375000 0.0448627 0.92783
-500000 0.0354542 0.942565
-625000 0.0262361 0.957186
-750000 0.0191283 0.968602
-875000 0.0143646 0.976313
-1000000 0.0119458 0.980266
-1125000 0.0101314 0.983245
-1250000 0.00746224 0.987643
-1375000 0.00571069 0.990536
-1500000 0.00391978 0.9935
-1625000 0.00247309 0.995906
-1750000 0.00100795 0.998349
-1875000 -0.000337302 1.0006
-2000000 -0.00185 1.00313
-2125000 -0.00317507 1.00536
-2250000 -0.00454804 1.00768
-2375000 -0.00589512 1.00995
-2500000 -0.00702757 1.01187
+125000 0.0632017 0.899723
+250000 0.0561376 0.910429
+375000 0.0471384 0.924277
+500000 0.0349153 0.943416
+625000 0.0244399 0.960071
+750000 0.019451 0.968073
+875000 0.0134728 0.977767
+1000000 0.011723 0.980628
+1125000 0.00945656 0.984351
+1250000 0.00790634 0.986905
+1375000 0.00564311 0.990642
+1500000 0.00376572 0.993753
+1625000 0.00238483 0.996053
+1750000 0.00085649 0.9986
+1875000 -0.000515888 1.0009
+2000000 -0.00151569 1.00257
+2125000 -0.00325174 1.00549
+2250000 -0.00472612 1.00798
+2375000 -0.00578231 1.00976
+2500000 -0.00729864 1.01233

examples/USER/fep/CC-CO/fdti10/in.fdti10.lmp

@@ -67,7 +67,7 @@ neighbor 2.0 bin
 
 timestep 2.0
 
-# velocity all create ${temp} 12345
+velocity all create ${temp} 12345
 
 thermo_style multi
 thermo ${nprint}

examples/USER/fep/CC-CO/fep01/fep01.lmp

@@ -1,22 +1,22 @@
 # Time-averaged data for fix fFEP
 # TimeStep c_cFEP[1] c_cFEP[2]
-125000 0.204052 0.716278
-250000 0.170933 0.757733
-375000 0.131428 0.810827
-500000 0.104001 0.849005
-625000 0.0742666 0.895019
-750000 0.0368268 0.956361
-875000 0.00854967 1.00673
-1000000 -0.0285584 1.07433
-1125000 -0.0566901 1.13072
-1250000 -0.100832 1.23058
-1375000 -0.144906 1.3401
-1500000 -0.187874 1.44338
-1625000 -0.242872 1.59879
-1750000 -0.2946 1.75277
-1875000 -0.365817 2.01194
-2000000 -0.440188 2.35835
-2125000 -0.642098 3.47641
-2250000 -0.88601 5.57546
-2375000 -1.10314 8.00578
-2500000 -1.371 12.5211
+125000 0.205889 0.714253
+250000 0.164934 0.765732
+375000 0.131935 0.809532
+500000 0.09771 0.859006
+625000 0.0688602 0.903005
+750000 0.0356141 0.958919
+875000 -0.00180317 1.02349
+1000000 -0.0317681 1.08115
+1125000 -0.0686221 1.15601
+1250000 -0.117495 1.2677
+1375000 -0.140627 1.31823
+1500000 -0.179791 1.41782
+1625000 -0.233651 1.57071
+1750000 -0.284345 1.71981
+1875000 -0.367527 2.01219
+2000000 -0.480496 2.54915
+2125000 -0.644218 3.47978
+2250000 -0.898797 5.57997
+2375000 -1.1516 8.56702
+2500000 -1.36364 12.2295

examples/USER/fep/CC-CO/fep01/in.fep01

@@ -0,0 +1,143 @@
+# created by fftool
+
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+special_bonds lj/coul 0.0 0.0 0.5
+
+read_data data.0.lmp
+# read_restart restart.*.lmp
+# reset_timestep 0
+
+pair_style hybrid lj/cut/coul/long 10.0 10.0 &
+  lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
+pair_modify tail no
+kspace_style pppm 1.0e-4
+
+pair_coeff    1    1  none  # C-CO C-CO
+pair_coeff    1    2  none  # C-CO C-D
+pair_coeff    1    3  none  # C-CO H-D
+pair_coeff    1    4  none  # C-CO H-H1
+pair_coeff    1    5  none  # C-CO OHD-
+pair_coeff    1    6  none  # C-CO HOD-
+pair_coeff    1    7  lj/cut/coul/long    0.0000   1.0000  # C-CO Hw
+pair_coeff    1    8  lj/cut/coul/long    0.1013   3.3286  # C-CO Ow
+pair_coeff    2    2  none  # C-D C-D
+pair_coeff    2    3  none  # C-D H-D
+pair_coeff    2    4  none  # C-D H-H1
+pair_coeff    2    5  none  # C-D OHD-
+pair_coeff    2    6  none  # C-D HOD-
+pair_coeff    2    7  lj/cut/coul/long/soft    0.0000   1.0000  1.0  # C-D Hw
+pair_coeff    2    8  lj/cut/coul/long/soft    0.1013   3.3286  1.0  # C-D Ow
+pair_coeff    3    3  none  # H-D H-D
+pair_coeff    3    4  lj/cut/coul/long/soft    0.0300   2.5000  1.0  # H-D H-H1
+pair_coeff    3    5  none  # H-D OHD-
+pair_coeff    3    6  none  # H-D HOD-
+pair_coeff    3    7  lj/cut/coul/long/soft    0.0000   1.0000  1.0  # H-D Hw
+pair_coeff    3    8  lj/cut/coul/long/soft    0.0683   2.8131  1.0  # H-D Ow
+pair_coeff    4    4  none  # H-H1 H-H1
+pair_coeff    4    5  none  # H-H1 OHD-
+pair_coeff    4    6  lj/cut/coul/long/soft    0.0000   1.0000  0.0 # H-H1 HOD-
+pair_coeff    4    7  lj/cut/coul/long    0.0000   1.0000  # H-H1 Hw
+pair_coeff    4    8  lj/cut/coul/long    0.0683   2.8131  # H-H1 Ow
+pair_coeff    5    5  none  # OHD- OHD-
+pair_coeff    5    6  none  # OHD- HOD-
+pair_coeff    5    7  lj/cut/coul/long/soft    0.0000   1.0000  0.0  # OHD- Hw
+pair_coeff    5    8  lj/cut/coul/long/soft    0.1625   3.1427  0.0  # OHD- Ow
+pair_coeff    6    6  none  # HOD- HOD-
+pair_coeff    6    7  lj/cut/coul/long/soft    0.0000   1.0000  0.0  # HOD- Hw
+pair_coeff    6    8  lj/cut/coul/long/soft    0.0000   1.7792  0.0  # HOD- Ow
+pair_coeff    7    7  lj/cut/coul/long    0.0000   1.0000  # Hw Hw
+pair_coeff    7    8  lj/cut/coul/long    0.0000   1.0000  # Hw Ow
+pair_coeff    8    8  lj/cut/coul/long    0.1554   3.1655  # Ow Ow
+
+variable nsteps equal 25000
+variable nprint equal ${nsteps}/500
+variable ndump equal ${nsteps}/100
+# variable nrestart equal ${nsteps}/10
+
+variable temp equal 300.0
+variable press equal 1.0
+
+neighbor 2.0 bin
+
+timestep 2.0
+
+# velocity all create ${temp} 12345
+
+thermo_style multi
+thermo ${nprint}
+
+fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
+
+fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
+
+run 10000
+reset_timestep 0
+write_restart  init.restart
+
+
+variable lambda equal ramp(0.0,1.0)
+variable minusl equal 1.0-v_lambda
+variable q1 equal  0.145*v_lambda-0.180*(1.0-v_lambda)
+variable q2 equal -0.180*(1.0-v_lambda)
+variable q3 equal  0.060*(1.0-v_lambda)
+variable q4 equal  0.040*v_lambda+0.060*(1.0-v_lambda)
+variable q5 equal -0.683*v_lambda
+variable q6 equal  0.418*v_lambda
+
+fix fADAPT all adapt/fep 125000 &
+    pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusl &
+    pair lj/cut/coul/long/soft lambda 3 4 v_minusl &
+    pair lj/cut/coul/long/soft lambda 4 6 v_lambda &
+    pair lj/cut/coul/long/soft lambda 5*6 7*8 v_lambda &
+    atom charge 1 v_q1 &
+    atom charge 2 v_q2 &
+    atom charge 3 v_q3 &
+    atom charge 4 v_q4 &
+    atom charge 5 v_q5 &
+    atom charge 6 v_q6 &
+    after yes
+
+variable dlambda equal 0.05
+variable minusdl equal -0.05
+variable dq1 equal  0.145*v_dlambda+0.180*v_dlambda
+variable dq2 equal  0.180*v_dlambda
+variable dq3 equal -0.060*v_dlambda
+variable dq4 equal  0.040*v_dlambda-0.060*v_dlambda
+variable dq5 equal -0.683*v_dlambda
+variable dq6 equal  0.418*v_dlambda
+
+compute cFEP all fep ${temp} &
+    pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
+    pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
+    pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
+    pair lj/cut/coul/long/soft lambda 5*6 7*8 v_dlambda &
+    atom charge 1 v_dq1 &
+    atom charge 2 v_dq2 &
+    atom charge 3 v_dq3 &
+    atom charge 4 v_dq4 &
+    atom charge 5 v_dq5 &
+    atom charge 6 v_dq6
+
+fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fep01.lmp
+
+# compute cRDF all rdf 100 1 1
+# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
+
+compute cMSD all msd
+fix fMSD all 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 C H H O H H O
+
+# restart ${nrestart} restart.*.lmp
+
+run ${nsteps}
+
+write_restart restart.*.lmp
+write_data data.*.lmp

examples/USER/fep/CC-CO/fep01/in.fep01.lmp

@@ -67,7 +67,7 @@ neighbor 2.0 bin
 
 timestep 2.0
 
-# velocity all create ${temp} 12345
+velocity all create ${temp} 12345
 
 thermo_style multi
 thermo ${nprint}

examples/USER/fep/CC-CO/fep10/fep10.lmp

@@ -1,22 +1,22 @@
 # Time-averaged data for fix fFEP
 # TimeStep c_cFEP[1] c_cFEP[2]
-125000 1.61722 0.0816181
-250000 1.4554 0.108446
-375000 1.12276 0.187761
-500000 0.882162 0.274771
-625000 0.654849 0.384243
-750000 0.480932 0.495323
-875000 0.368114 0.579941
-1000000 0.307984 0.63715
-1125000 0.264054 0.683279
-1250000 0.193663 0.761243
-1375000 0.146131 0.817137
-1500000 0.0980797 0.876785
-1625000 0.0597639 0.930022
-1750000 0.0209208 0.987792
-1875000 -0.0146947 1.04379
-2000000 -0.0540298 1.11055
-2125000 -0.0886095 1.17399
-2250000 -0.124106 1.24444
-2375000 -0.1586 1.31721
-2500000 -0.187727 1.38222
+125000 1.6302 0.0823708
+250000 1.42237 0.11283
+375000 1.1798 0.168088
+500000 0.869449 0.279336
+625000 0.610803 0.412455
+750000 0.489597 0.486584
+875000 0.34439 0.601048
+1000000 0.303411 0.640696
+1125000 0.244627 0.70206
+1250000 0.204737 0.746389
+1375000 0.144716 0.816302
+1500000 0.0941156 0.880968
+1625000 0.0575351 0.933564
+1750000 0.0171831 0.992497
+1875000 -0.018964 1.05078
+2000000 -0.0457397 1.09726
+2125000 -0.0904898 1.17888
+2250000 -0.128205 1.25226
+2375000 -0.155891 1.31122
+2500000 -0.194237 1.3965

examples/USER/fep/CC-CO/fep10/in.fep10.lmp

@@ -67,7 +67,7 @@ neighbor 2.0 bin
 
 timestep 2.0
 
-# velocity all create ${temp} 12345
+velocity all create ${temp} 12345
 
 thermo_style multi
 thermo ${nprint}

examples/USER/fep/CC-CO/mols/README.md

@@ -0,0 +1,15 @@
+Ethane to Methanol Molecule Files
+=================================
+
+Files necessary to build starting configurations using the
+[fftool.py](http://www.github.com/agiliopadua/fftool) utility and
+[Packmol](http://www.ime.unicamp.br/~martinez/packmol/), for example:
+
+    fftool.py 1 CC-CO.zmat 360 spce.zmat -r 50
+
+    packmol < pack.in
+
+    fftool.py 1 CC-CO.zmat 360 spce.zmat -r 50 -l -a
+
+The resulting `in.lmp` files have to be modified to introduce the free
+energy route.

examples/USER/fep/CH4-CF4/README.md

@@ -0,0 +1,57 @@
+Methane to Tetrafluoromethane in Water
+======================================
+
+Example calculation of the difference in free energy of hydration upon
+transforming methane into tetrafluoromethane with LAMMPS using
+*compute fep* and *fix adapt*.
+
+Methane and tetrafluoromethane are represented by the OPLS-AA force
+field (1 molecule). Water is represented by the 3-site SPC/E model
+(360 molecules).
+
+The strategy used to perform the alchemical transformation is the
+following:
+
+* The dual topology approach is used, therefore all the atoms of
+  methane and perfluorommethane are present throughout the simulation,
+  only some of them are dummy sites at the endpoints of the
+  transformation. Masses and intramolecular terms (bond lengths,
+  angles, dihedrals) are not changed.
+
+* Interactions of sites that are being created (from dummy sites) or
+  deleted (to become dummy sites) are treated using soft-core verions
+  of the Lennard-Jones and Coulomb potentials (*pair
+  lj/cut/coul/long/soft*) in order to avoid singularities. The
+  exponent of the coupling parameter lambda in the soft-core pair
+  potentials was in this example n = 1.
+
+* Eletrostatic charges that are modified are varied linearly from the
+  initial to the final values. This keeps the overall charge of the
+  molecule constant, which is good for the long range electrostatics
+  (the coupling parameter lambda has no effect on the kspace terms).
+
+The following directories contain input files and results for
+calculations using Bennet's acceptance ratio (BAR) method:
+
+* `bar01` -- Calculation using BAR, 1-step transformation of a CH4
+  molecule into CF4. Results in `bar01.lmp`
+
+* `bar10` -- Calculation using BAR, 1-step transformation of a
+  CF4 molecule into CH4. Results in `bar10.lmp`
+
+The Python script `bar.py` found in the `tools` directory can
+be used to calculate the free-energy difference corresponding to the
+transformation:
+
+    bar.py 300 bar01.lmp bar10.lmp
+
+The outputs are in kcal/mol and can be compared with the experimental
+value of 1.2 kcal/mol and with a simulation value from the literature
+(using a different force field): 0.8 kcal/mol
+[Gough, Pearlman, Kolmann, J Chem Phys 99 (1993) 9103]. This small
+free energy difference is difficult to predict.
+
+These example calculations are for tutorial purposes only. The results
+may not be of research quality (not enough sampling, size of the step
+in lambda or of the delta for numerical derivative not optimized, no
+evaluation of ideal-gas contributions, etc.)

examples/USER/fep/CH4hyd/README

@@ -2,7 +2,7 @@ Free Energy of Hydration of Methane
 ===================================
 
 Example calculation of the free energy of hydration of methane with
-LAMMPS using *compute fep* and *fix adapt*.
+LAMMPS using *compute fep* and *fix adapt/fep*.
 
 Methane is represented by the 5-site OPLS-AA model (1 molecule). Water
 is represented by the 4-site TIP4P-Ew model (360 molecules). Interactions

examples/USER/fep/CH4hyd/fdti01/fdti01.lmp

@@ -1,22 +1,22 @@
 # Time-averaged data for fix fFEP
 # TimeStep c_cFEP[1] c_cFEP[2]
-125000 0.000446819 0.999261
-250000 0.00616472 0.989735
-375000 0.0134402 0.977764
-500000 0.0212226 0.965209
-625000 0.0268231 0.956445
-750000 0.0187644 0.969568
-875000 0.0159261 0.974132
-1000000 0.00775701 0.987344
-1125000 0.00565507 0.990774
-1250000 0.00353241 0.994238
-1375000 0.00203707 0.996707
-1500000 0.00050588 0.999235
-1625000 -0.000372564 1.00069
-1750000 -0.00191033 1.00326
-1875000 -0.00228176 1.00388
-2000000 -0.00294996 1.00499
-2125000 -0.00358192 1.00605
-2250000 -0.00450789 1.0076
-2375000 -0.00518595 1.00875
-2500000 -0.00598456 1.01009
+125000 0.000490778 0.999186
+250000 0.00619786 0.989679
+375000 0.0128045 0.978813
+500000 0.0203102 0.96667
+625000 0.0272161 0.955808
+750000 0.0215735 0.965087
+875000 0.0148509 0.975821
+1000000 0.00936378 0.984752
+1125000 0.00490088 0.992007
+1250000 0.00388501 0.99366
+1375000 0.00122887 0.998043
+1500000 0.000498063 0.999247
+1625000 -0.000468616 1.00085
+1750000 -0.00131731 1.00226
+1875000 -0.00247035 1.00419
+2000000 -0.00306799 1.00519
+2125000 -0.00355565 1.006
+2250000 -0.00434289 1.00733
+2375000 -0.00497634 1.00839
+2500000 -0.00576373 1.00972

examples/USER/fep/CH4hyd/fdti01/in.fdti01.lmp

@@ -43,7 +43,7 @@ neighbor 2.0 bin
 
 timestep 2.0
 
-# velocity all create ${temp} 12345
+velocity all create ${temp} 12345
 
 thermo_style multi
 thermo ${nprint}

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

@@ -1,22 +1,22 @@
 # Time-averaged data for fix fFEP
 # TimeStep c_cFEP[1] c_cFEP[2]
-125000 0.00662676 0.988949
-250000 0.00577009 0.990374
-375000 0.00509787 0.991495
-500000 0.00423066 0.992943
-625000 0.00355797 0.994072
-750000 0.00300236 0.995005
-875000 0.00207026 0.996574
-1000000 0.0012208 0.998006
-1125000 0.000294349 0.999569
-1250000 -0.00048893 1.0009
-1375000 -0.00182937 1.00319
-1500000 -0.00310589 1.00538
-1625000 -0.00598809 1.01032
-1750000 -0.00952227 1.01643
-1875000 -0.0142065 1.02465
-2000000 -0.0204154 1.03549
-2125000 -0.0225356 1.03896
-2250000 -0.0203097 1.03482
-2375000 -0.0126704 1.02155
-2500000 -0.00585896 1.0099
+125000 0.00652155 0.989123
+250000 0.00572718 0.990445
+375000 0.00506788 0.991544
+500000 0.00448303 0.992522
+625000 0.00370796 0.993818
+750000 0.00277535 0.995385
+875000 0.00230833 0.996171
+1000000 0.000982551 0.998409
+1125000 0.000314678 0.99954
+1250000 -0.000839025 1.0015
+1375000 -0.00155615 1.00273
+1500000 -0.00320598 1.00553
+1625000 -0.00587133 1.01011
+1750000 -0.00867306 1.01495
+1875000 -0.0134768 1.02327
+2000000 -0.0229314 1.03995
+2125000 -0.0282333 1.04896
+2250000 -0.0202762 1.03477
+2375000 -0.0123279 1.02096
+2500000 -0.00546203 1.00923

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

@@ -43,7 +43,7 @@ neighbor 2.0 bin
 
 timestep 2.0
 
-# velocity all create ${temp} 12345
+velocity all create ${temp} 12345
 
 thermo_style multi
 thermo ${nprint}

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 0.0785579 0.884485
-250000 0.249497 0.672474
-375000 0.468227 0.483171
-500000 0.699558 0.374081
-625000 0.86155 0.34934
-750000 0.603327 0.529765
-875000 0.506332 0.584693
-1000000 0.255037 0.774695
-1125000 0.187388 0.834124
-1250000 0.120545 0.896585
-1375000 0.0742771 0.949163
-1500000 0.0284744 1.00256
-1625000 0.00160496 1.0359
-1750000 -0.0416872 1.10122
-1875000 -0.0538419 1.12112
-2000000 -0.0735692 1.14871
-2125000 -0.0918409 1.17959
-2250000 -0.11692 1.22543
-2375000 -0.135597 1.2613
-2500000 -0.156444 1.30333
+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

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

@@ -43,7 +43,7 @@ neighbor 2.0 bin
 
 timestep 2.0
 
-# velocity all create ${temp} 12345
+velocity all create ${temp} 12345
 
 thermo_style multi
 thermo ${nprint}

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 0.158566 0.768362
-250000 0.137898 0.79724
-375000 0.122731 0.819524
-500000 0.102845 0.850519
-625000 0.0883504 0.875931
-750000 0.0769041 0.896381
-875000 0.0566024 0.93535
-1000000 0.0386503 0.969383
-1125000 0.0191582 1.00842
-1250000 0.0039511 1.04642
-1375000 -0.0238638 1.11807
-1500000 -0.0487045 1.19757
-1625000 -0.107949 1.37985
-1750000 -0.179094 1.65366
-1875000 -0.272974 2.18722
-2000000 -0.396083 2.7182
-2125000 -0.432495 2.47978
-2250000 -0.379414 2.0193
-2375000 -0.216989 1.48135
-2500000 -0.0722148 1.13936
+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

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

@@ -43,7 +43,7 @@ neighbor 2.0 bin
 
 timestep 2.0
 
-# velocity all create ${temp} 12345
+velocity all create ${temp} 12345
 
 thermo_style multi
 thermo ${nprint}