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update to USER-FEP docs and examples

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This commit is contained in:
Axel Kohlmeyer
2015-05-15 00:59:50 -04:00
parent f084911239
commit 21db4bc68c
15 changed files with 10766 additions and 20422 deletions
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2
doc/Section_packages.txt
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@ -119,7 +119,7 @@ USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sd
USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (3), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_accelerate_cuda.html, USER/cuda, -, lib/cuda
USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "fix adapt/fep"_fix_adapt.html, USER/fep, -, -
USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -
USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, -
USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, -
USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -

2
doc/compute_fep.txt
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@ -23,7 +23,7 @@ attribute = {pair} or {atom} :l
I,J = type pair(s) to set parameter for
v_delta = variable with perturbation to apply (in the units of the parameter)
{atom} args = aparam I v_delta
aparam = parameter to adapt over time
aparam = parameter to perturb
I = type to set parameter for
v_delta = variable with perturbation to apply (in the units of the parameter) :pre
zero or more keyword/value pairs may be appended :l

86
doc/pair_lj_soft.txt
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@ -106,12 +106,12 @@ pair_coeff 1 1 1.0 9.5 :pre
The {lj/cut/soft} style and substyles compute the 12/6 Lennard-Jones
and Coulomb potential modified by a soft core, in order to avoid
singularities during free energy calculations when sites are created
or anihilated "(Beutler)"_#Beutler.
or anihilated "(Beutler)"_#Beutler,
:c,image(Eqs/pair_lj_soft.jpg)
Coulomb interactions are also damped with a soft core at short
distance as
distance,
:c,image(Eqs/pair_coul_soft.jpg)
@ -120,11 +120,11 @@ are the charges on the 2 atoms, and epsilon is the dielectric constant
which can be set by the "dielectric"_dielectric.html command.
The coefficient lambda is an activation parameter. When lambda = 1 the
pair potentiel is identical to a Lennard-Jones term plus a Coulomb
term. When lambda = 0 the pair interactions are deactivated. The
transition between these two extrema is smoothed by a repulsive soft
core in order to avoid singularities in potential energy and forces
when sites are created or anihilated and can overlap
pair potentiel is identical to a Lennard-Jones term or a Coulomb term
or a combination of both. When lambda = 0 the interactions are
deactivated. The transition between these two extrema is smoothed by a
soft repulsive core in order to avoid singularities in potential
energy and forces when sites are created or anihilated and can overlap
"(Beutler)"_#Beutler.
The paratemers n, alpha_LJ and alpha_C are set in the
@ -132,11 +132,34 @@ The paratemers n, alpha_LJ and alpha_C are set in the
choices for the exponent are n = 2 or n = 1. For the remaining
coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are
appropriate choices. Plots of the LJ and Coulomb terms are shown
below, for lambda ranging from 1 ro 0 every 0.1.
below, for lambda ranging from 1 to 0 every 0.1.
:c,image(JPG/lj_soft.jpg),image(JPG/coul_soft.jpg)
The {lj/cut/tip4p/long/soft} implements a soft-core version of the
For the {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} pair styles,
the following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
epsilon (energy units)
sigma (distance units)
lambda (activation parameter between 0 and 1)
cutoff1 (distance units)
cutoff2 (distance units) :ul
The latter two coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair. You cannot specify 2 cutoffs for style {lj/cut/soft},
since it has no Coulombic terms. For the {coul/cut/soft} and
{coul/long/soft} only lambda and the optional cutoff2 are to be
specified.
Style {lj/cut/tip4p/long/soft} implements a soft-core version of the
TIP4P water model. The usage of this pair style is documented in the
"pair_lj"_pair_lj.html styles. The soft-core version introduces the
lambda parameter to the list of arguments, after epsilon and sigma in
@ -165,28 +188,18 @@ occur. These substyles are suitable to represent charges embedded in
the Lennard-Jones radius of another site (for example hydrogen atoms
in several water models).
For the {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} pair styles,
the following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
epsilon (energy units)
sigma (distance units)
lambda (activation parameter between 0 and 1)
cutoff1 (distance units)
cutoff2 (distance units) :ul
The latter two coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair. You cannot specify 2 cutoffs for style {lj/cut/soft},
since it has no Coulombic terms. For the {coul/cut/soft} and
{coul/long/soft} only lambda and the optional cutoff2 are to be
specified.
IMPORTANT NOTES: When using the core-softed Coulomb potentials with
long-range solvers ({coul/long/soft}, {lj/cut/coul/long/soft}, etc.)
in a free energy calculation in which sites holding electrostatic
charges are being created or anihilated (using
"fix_adapt/fep"_fix_adapt_fep.html and "compute_fep"_compute_fep.html)
it is important to adapt both the lambda activation parameter (from 0
to 1, or the reverse) and the value of the charge (from 0 to its final
value, or the reverse). This ensures that long-range electrostatic
terms (kspace) are correct. It is not necessary to use core-softed
Coulomb potentials if the van der Waals site is present during the
free-energy route, thus avoiding overlap of the charges. Examples are
provided in the LAMMPS source directory tree, under examples/USER/fep.
:line
@ -236,9 +249,14 @@ to be specified in an input script that reads a restart file.
[Restrictions:]
To avoid division by zero do not set sigma = 0. When sites do not
interact though the Lennard-Jones term use epsilon = 0 and sigma = 1
for example, or else use the {coul/long/soft} or similar substyle.
To avoid division by zero do not set sigma = 0; use the lambda
parameter instead to activate/deactivate interactions, or use
epsilon = 0 and sigma = 1. Alternatively, when sites do not
interact though the Lennard-Jones term the {coul/long/soft} or
similar substyle can be used via the
"pair_style hybrid/overlay"_pair_hybrid.html command.
:line
All of the plain {soft} pair styles are part of the USER-FEP package.
The {long} styles also requires the KSPACE package to be installed.

44
examples/USER/fep/CH4hyd/fdti01/fdti01.lmp
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@ -1,22 +1,22 @@
# Time-averaged data for fix fFEP
# TimeStep c_cFEP[1] c_cFEP[2]
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
# Time-averaged data for fix FEP
# TimeStep c_FEP[1] c_FEP[2]
100000 0.000289416 0.999521
200000 0.00590502 0.990163
300000 0.0115179 0.980934
400000 0.0216052 0.96457
500000 0.0222451 0.963797
600000 0.0200038 0.967603
700000 0.0152292 0.975176
800000 0.00896315 0.985384
900000 0.00585213 0.990434
1000000 0.00327599 0.99467
1100000 0.00159845 0.997437
1200000 0.000171108 0.999804
1300000 -0.000313183 1.00059
1400000 -0.00148 1.00254
1500000 -0.00297976 1.00504
1600000 -0.00287926 1.00487
1700000 -0.00430671 1.00727
1800000 -0.00453729 1.00765
1900000 -0.00507356 1.00856
2000000 -0.00586954 1.0099

53
examples/USER/fep/CH4hyd/fdti01/in.fdti01.lmp
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@ -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 0.002
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 fdti01.lmp
fix FEP all ave/time 20 4000 100000 c_FEP[1] c_FEP[2] file fdti01.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

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examples/USER/fep/CH4hyd/fdti01/log.lammps
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44
examples/USER/fep/CH4hyd/fdti10/fdti10.lmp
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@ -1,22 +1,22 @@
# Time-averaged data for fix fFEP
# TimeStep c_cFEP[1] c_cFEP[2]
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
# Time-averaged data for fix FEP
# TimeStep c_FEP[1] c_FEP[2]
100000 0.00671766 0.988799
200000 0.00591179 0.990139
300000 0.00495535 0.991733
400000 0.00428164 0.992859
500000 0.00367253 0.993879
600000 0.00334988 0.994424
700000 0.00246906 0.995908
800000 0.00139088 0.997725
900000 0.000491084 0.99924
1000000 0.000615407 0.999044
1100000 -0.00172714 1.00302
1200000 -0.00333962 1.00579
1300000 -0.0040424 1.00699
1400000 -0.0102385 1.01763
1500000 -0.0173611 1.03006
1600000 -0.0243837 1.04234
1700000 -0.0211518 1.03654
1800000 -0.0220119 1.03776
1900000 -0.013304 1.02261
2000000 -0.00648381 1.01095

52
examples/USER/fep/CH4hyd/fdti10/in.fdti10.lmp
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@ -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 -0.002
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 fdti10.lmp
fix FEP all ave/time 20 4000 100000 c_FEP[1] c_FEP[2] file fdti10.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

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examples/USER/fep/CH4hyd/fdti10/log.lammps
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44
examples/USER/fep/CH4hyd/fep01/fep01.lmp
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@ -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

53
examples/USER/fep/CH4hyd/fep01/in.fep01.lmp
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@ -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

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examples/USER/fep/CH4hyd/fep01/log.lammps
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examples/USER/fep/CH4hyd/fep10/fep10.lmp
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@ -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

52
examples/USER/fep/CH4hyd/fep10/in.fep10.lmp
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@ -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

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examples/USER/fep/CH4hyd/fep10/log.lammps
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