diff --git a/examples/USER/plumed/check-plumed.sh b/examples/USER/plumed/check-plumed.sh deleted file mode 100755 index b1b599f15c..0000000000 --- a/examples/USER/plumed/check-plumed.sh +++ /dev/null @@ -1,89 +0,0 @@ -# Needs make yes-molecule -# make yes-rigid -# make yes-kspace -# make yes-user-plumed ( obviously ) - - -#!/bin/bash - -LAMMPS=../../../src/lmp_mpi - -# Run first LAMMPS calculation -$LAMMPS < in.peptide-plumed - -# Check PLUMED positions -nlines=`paste plumed.xyz lammps.xyz | awk '{if( $2<$6-0.0001 || $2>$6+0.0001 || $3<$7-0.0001 || $3>$7+0.0001 || $4<$8-0.0002 || $4>$8+0.0002 ) if( $5!="Timestep:" && $1!=2004 ) print $0}' | wc -l` -if [ "$nlines" -gt 0 ] ; then - echo ERROR passing positions from LAMMPS to PLUMED - paste plumed.xyz lammps.xyz | awk '{if( $2<$6-0.0001 || $2>$6+0.0001 || $3<$7-0.0001 || $3>$7+0.0001 || $4<$8-0.0002 || $4>$8+0.0002 ) if( $5!="Timestep:" && $1!=2004 ) print $0, $2-$6, $3-$7, $4-$8}' -fi - -# CHECK PLUMED timestep -tstep=`grep timestep in.peptide-plumed | awk '{print $2}'` -tstep=`echo $tstep \* 0.001 \* 10 | bc -l` -nlines=`wc -l plmd_energy | awk '{print $1}'` - -for ((i=3;i<$nlines;i++)); do - told=`head -n $(($i-1)) plmd_energy | tail -n 1 | awk '{print $1}'` - tnew=`head -n $i plmd_energy | tail -n 1 | awk '{print $1}'` - tdiff=`echo \( $tnew - $told - $tstep \) \> 0 | bc -l` - if [ $tdiff -gt 0 ] ; then - echo ERROR passing timestep from LAMMPS to PLUMED - fi -done - -# Check PLUMED energy -tail -n +2 plmd_energy > plmd_energy2 -nlines=`paste lammps_energy plmd_energy2 | tail -n +2 | awk '{if( $2<$4-0.0001 || $2>$4+0.0001 ) print $0}' | wc -l` -if [ "$nlines" -gt 0 ] ; then - echo ERROR passing potential energy from LAMMPS to PLUMED - paste lammps_energy plmd_energy2 | tail -n +2 | awk '{if( $2<$4-0.0001 || $2>$4+0.0001 ) print $0}' -fi -rm -f plmd_energy2 - -# Check PLMD mass and charge -nlines=`wc -l mq_lammps | awk '{print $1}'` -sline=`grep -n "mass q" mq_lammps | awk '{print $1}' | sed -e s/:ITEM://` -for ((i=$sline+1;i<$nlines;i++)); do - # Mass and charge from LAMMPS - index=`head -n $i mq_lammps | tail -n 1 | awk '{print $1}'` - l_mass=`head -n $i mq_lammps | tail -n 1 | awk '{print $2}'` - l_charge=`head -n $i mq_lammps | tail -n 1 | awk '{print $3}'` - # Mass and charge from PLUMED - p_mass=`head -n $(($index+1)) mq_plumed | tail -n 1 | awk '{print $2}'` - p_charge=`head -n $(($index+1)) mq_plumed | tail -n 1 | awk '{print $3}'` - # Check PLUMED mass is same as lammps mass - mdiff=`echo \( $l_mass - $p_mass \) \> 0 | bc -l` - if [ "$mdiff" -gt 0 ] ; then - echo ERROR passing masses from LAMMPS to PLUMED - fi - # Check PLUMED charge is same as lammps charge - qdiff=`echo \( $l_charge - $p_charge \) \> 0 | bc -l` - if [ "$qdiff" -gt 0 ] ; then - echo ERROR passing charges from LAMMPS to PLUMED - fi -done - -# Run calculations to test adding restraint on bond -$LAMMPS < in.peptide-plumed-plumed-restraint -$LAMMPS < in.peptide-plumed-lammps-restraint -# Now compare value of distance when lammps and plumed restraint the distance -nlines=`paste lammps_restraint plumed_restraint | tail -n +2 | awk '{if( $2<$4-0.0001 || $2>$4+0.0001 ) print $0}' | wc -l` -if [ "$nlines" -gt 0 ] ; then - echo ERROR passing forces from PLUMED back to LAMMPS -fi - -# Now run calculations to test virial -$LAMMPS < in.peptide-plumed-npt -$LAMMPS < in.peptide-plumed-npt2 - -nlines=`paste plmd_volume_with_restraint plmd_volume_without_restraint | tail -n +2 | awk '{if( $2<$4-0.0001 || $2>$4+0.0001 ) print $0}' | wc -l` -if [ "$nlines" -gt 0 ] ; then - echo ERROR passing virial from PLUMED back to LAMMPS -fi - -# Nothing from here works - -# Now run calculations to check forces on energy -$LAMMPS < in.peptide-plumed-engforce-ref -$LAMMPS < in.peptide-plumed-eng-force-plumed diff --git a/examples/USER/plumed/clear-files.sh b/examples/USER/plumed/clear-files.sh deleted file mode 100755 index 5e588146f7..0000000000 --- a/examples/USER/plumed/clear-files.sh +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -# Data from first set of checks -rm bck.* plmd_energy lammps_energy mq_plumed mq_lammps lammps.xyz plumed.xyz p.log -# Data from checks on restraints -rm bck.* p.log lammps_restraint plumed_restraint -# Data from checks on virial -rm bck.* lammps_energy lammps.xyz log.lammps plmd_volume p.log plmd_volume_without_restraint plmd_volume_with_restraint diff --git a/examples/USER/plumed/colvar b/examples/USER/plumed/colvar new file mode 100644 index 0000000000..df282364f5 --- /dev/null +++ b/examples/USER/plumed/colvar @@ -0,0 +1,103 @@ +#! FIELDS time dd + 0.000000 5.985554 + 0.002000 6.002880 + 0.004000 6.022015 + 0.006000 6.029922 + 0.008000 6.020103 + 0.010000 5.996906 + 0.012000 5.972734 + 0.014000 5.960079 + 0.016000 5.963714 + 0.018000 5.978140 + 0.020000 5.991813 + 0.022000 5.995155 + 0.024000 5.987021 + 0.026000 5.975340 + 0.028000 5.971456 + 0.030000 5.981945 + 0.032000 6.003550 + 0.034000 6.024743 + 0.036000 6.032990 + 0.038000 6.022936 + 0.040000 6.000131 + 0.042000 5.977800 + 0.044000 5.968692 + 0.046000 5.977224 + 0.048000 5.996934 + 0.050000 6.014800 + 0.052000 6.019586 + 0.054000 6.008803 + 0.056000 5.989809 + 0.058000 5.974484 + 0.060000 5.971140 + 0.062000 5.979074 + 0.064000 5.989379 + 0.066000 5.991356 + 0.068000 5.980176 + 0.070000 5.960625 + 0.072000 5.944401 + 0.074000 5.942614 + 0.076000 5.958402 + 0.078000 5.984574 + 0.080000 6.007964 + 0.082000 6.017667 + 0.084000 6.011795 + 0.086000 5.998304 + 0.088000 5.989405 + 0.090000 5.993275 + 0.092000 6.008545 + 0.094000 6.025183 + 0.096000 6.031186 + 0.098000 6.020651 + 0.100000 5.997952 + 0.102000 5.975230 + 0.104000 5.964757 + 0.106000 5.971150 + 0.108000 5.988568 + 0.110000 6.004676 + 0.112000 6.008731 + 0.114000 5.998481 + 0.116000 5.981406 + 0.118000 5.969615 + 0.120000 5.971827 + 0.122000 5.987658 + 0.124000 6.007888 + 0.126000 6.020477 + 0.128000 6.018377 + 0.130000 6.004046 + 0.132000 5.987682 + 0.134000 5.980338 + 0.136000 5.986534 + 0.138000 6.001303 + 0.140000 6.013589 + 0.142000 6.013717 + 0.144000 6.000028 + 0.146000 5.980283 + 0.148000 5.966836 + 0.150000 5.968670 + 0.152000 5.985459 + 0.154000 6.007612 + 0.156000 6.022374 + 0.158000 6.022034 + 0.160000 6.008851 + 0.162000 5.993355 + 0.164000 5.987212 + 0.166000 5.995452 + 0.168000 6.013111 + 0.170000 6.028386 + 0.172000 6.030387 + 0.174000 6.016468 + 0.176000 5.994191 + 0.178000 5.976616 + 0.180000 5.973983 + 0.182000 5.987185 + 0.184000 6.007275 + 0.186000 6.021338 + 0.188000 6.020837 + 0.190000 6.006955 + 0.192000 5.989433 + 0.194000 5.979796 + 0.196000 5.983601 + 0.198000 5.996921 + 0.200000 6.009310 + 0.202000 6.011114 diff --git a/examples/USER/plumed/in.peptide-plumed b/examples/USER/plumed/in.peptide-plumed index ef9d15b961..6972c0cfca 100644 --- a/examples/USER/plumed/in.peptide-plumed +++ b/examples/USER/plumed/in.peptide-plumed @@ -35,10 +35,7 @@ fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 thermo_style custom step temp etotal pe ke epair ebond f_2 thermo 10 -dump dd all xyz 10 lammps.xyz variable step equal step variable pe equal pe -fix 5 all print 10 "$(v_step) $(v_pe)" file lammps_energy -dump mq all custom 200 mq_lammps id mass q run 101 diff --git a/examples/USER/plumed/in.peptide-plumed-eng-force-plumed b/examples/USER/plumed/in.peptide-plumed-eng-force-plumed deleted file mode 100644 index e45fd0844a..0000000000 --- a/examples/USER/plumed/in.peptide-plumed-eng-force-plumed +++ /dev/null @@ -1,41 +0,0 @@ -# Solvated 5-mer peptide - -units real -atom_style full - -pair_style lj/charmm/coul/long 8.0 10.0 10.0 -bond_style harmonic -angle_style charmm -dihedral_style charmm -improper_style harmonic -kspace_style pppm 0.0001 - -read_data data.peptide - -neighbor 2.0 bin -neigh_modify delay 5 - -timestep 1.8181818181818181 - -group peptide type <= 12 -group one id 2 4 5 6 -group two id 80 82 83 84 -group ref id 37 -group colvar union one two ref - -fix 1 all nvt temp 363.0 363.0 90.90909090909091 tchain 1 - -fix 2 all plumed plumedfile plumed-engforce.dat outfile p.log - -#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz -#dump_modify 1 sort id - -thermo_style custom step temp etotal pe ke epair ebond f_2 -thermo 10 -dump dd all xyz 10 lammps.xyz -variable step equal step -variable pe equal pe -fix 5 all print 10 "$(v_step) $(v_pe)" file lammps_energy -dump mq all custom 200 mq_lammps id mass q - -run 101 diff --git a/examples/USER/plumed/in.peptide-plumed-engforce-ref b/examples/USER/plumed/in.peptide-plumed-engforce-ref deleted file mode 100644 index d812e2b015..0000000000 --- a/examples/USER/plumed/in.peptide-plumed-engforce-ref +++ /dev/null @@ -1,40 +0,0 @@ -# Solvated 5-mer peptide - -units real -atom_style full - -pair_style lj/charmm/coul/long 8.0 10.0 10.0 -bond_style harmonic -angle_style charmm -dihedral_style charmm -improper_style harmonic -kspace_style pppm 0.0001 - -read_data data.peptide - -neighbor 2.0 bin -neigh_modify delay 5 - -timestep 2.0 - -group peptide type <= 12 -group one id 2 4 5 6 -group two id 80 82 83 84 -group ref id 37 -group colvar union one two ref - -fix 1 all nvt temp 300.0 300.0 100.0 tchain 1 - -fix 2 all plumed plumedfile plumed-eng-ref.dat outfile p.log - -#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz -#dump_modify 1 sort id - -thermo_style custom step temp etotal pe ke epair ebond f_2 -thermo 10 -dump dd all xyz 10 lammps.xyz -variable step equal step -variable pe equal pe -dump mq all custom 200 mq_lammps id mass q - -run 101 diff --git a/examples/USER/plumed/in.peptide-plumed-lammps-restraint b/examples/USER/plumed/in.peptide-plumed-lammps-restraint deleted file mode 100644 index 3476c76b22..0000000000 --- a/examples/USER/plumed/in.peptide-plumed-lammps-restraint +++ /dev/null @@ -1,44 +0,0 @@ -# Solvated 5-mer peptide - -units real -atom_style full - -pair_style lj/charmm/coul/long 8.0 10.0 10.0 -bond_style harmonic -angle_style charmm -dihedral_style charmm -improper_style harmonic -kspace_style pppm 0.0001 - -read_data data.peptide - -neighbor 2.0 bin -neigh_modify delay 5 - -timestep 2.0 - -group peptide type <= 12 -group one id 2 4 5 6 -group two id 80 82 83 84 -group ref id 37 -group colvar union one two ref - -fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 -fix 6 all restrain bond 45 48 1000.0 1000.0 6.0 -fix 2 all plumed plumedfile plumed-norestraint.dat outfile p.log -fix 2a ref setforce 0.0 0.0 0.0 - -fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 - -#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz -#dump_modify 1 sort id - -thermo_style custom step temp etotal pe ke epair ebond f_2 -thermo 10 -dump dd all xyz 10 lammps.xyz -variable step equal step -variable pe equal pe -fix 5 all print 10 "$(v_step) $(v_pe)" file lammps_energy -dump mq all custom 200 mq_lammps id mass q - -run 101 diff --git a/examples/USER/plumed/in.peptide-plumed-npt b/examples/USER/plumed/in.peptide-plumed-npt deleted file mode 100644 index 1fe9e0c2fa..0000000000 --- a/examples/USER/plumed/in.peptide-plumed-npt +++ /dev/null @@ -1,43 +0,0 @@ -# Solvated 5-mer peptide - -units real -atom_style full - -pair_style lj/charmm/coul/long 8.0 10.0 10.0 -bond_style harmonic -angle_style charmm -dihedral_style charmm -improper_style harmonic -kspace_style pppm 0.0001 - -read_data data.peptide - -neighbor 2.0 bin -neigh_modify delay 5 - -timestep 2.0 - -group peptide type <= 12 -group one id 2 4 5 6 -group two id 80 82 83 84 -group ref id 37 -group colvar union one two ref - -fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 -fix 1 all npt temp 275.0 275.0 100.0 iso 0.987 0.987 400.0 tchain 1 - -fix 2 all plumed plumedfile plumed_npt.dat outfile p.log -fix 2a ref setforce 0.0 0.0 0.0 - -#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz -#dump_modify 1 sort id - -thermo_style custom step temp etotal pe ke epair ebond f_2 -thermo 10 -dump dd all xyz 10 lammps.xyz -variable step equal step -variable pe equal pe -fix 5 all print 10 "$(v_step) $(v_pe)" file lammps_energy -dump mq all custom 200 mq_lammps id mass q - -run 101 diff --git a/examples/USER/plumed/in.peptide-plumed-npt2 b/examples/USER/plumed/in.peptide-plumed-npt2 deleted file mode 100644 index 984407d1e8..0000000000 --- a/examples/USER/plumed/in.peptide-plumed-npt2 +++ /dev/null @@ -1,43 +0,0 @@ -# Solvated 5-mer peptide - -units real -atom_style full - -pair_style lj/charmm/coul/long 8.0 10.0 10.0 -bond_style harmonic -angle_style charmm -dihedral_style charmm -improper_style harmonic -kspace_style pppm 0.0001 - -read_data data.peptide - -neighbor 2.0 bin -neigh_modify delay 5 - -timestep 2.0 - -group peptide type <= 12 -group one id 2 4 5 6 -group two id 80 82 83 84 -group ref id 37 -group colvar union one two ref - -fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 -fix 1 all npt temp 275.0 275.0 100.0 iso 987.9 987.9 400.0 tchain 1 - -fix 2 all plumed plumedfile plumed_npt2.dat outfile p.log -fix 2a ref setforce 0.0 0.0 0.0 - -#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz -#dump_modify 1 sort id - -thermo_style custom step temp etotal pe ke epair ebond f_2 -thermo 10 -dump dd all xyz 10 lammps.xyz -variable step equal step -variable pe equal pe -fix 5 all print 10 "$(v_step) $(v_pe)" file lammps_energy -dump mq all custom 200 mq_lammps id mass q - -run 101 diff --git a/examples/USER/plumed/in.peptide-plumed-plumed-restraint b/examples/USER/plumed/in.peptide-plumed-plumed-restraint deleted file mode 100644 index 8ce35dd720..0000000000 --- a/examples/USER/plumed/in.peptide-plumed-plumed-restraint +++ /dev/null @@ -1,44 +0,0 @@ -# Solvated 5-mer peptide - -units real -atom_style full - -pair_style lj/charmm/coul/long 8.0 10.0 10.0 -bond_style harmonic -angle_style charmm -dihedral_style charmm -improper_style harmonic -kspace_style pppm 0.0001 - -read_data data.peptide - -neighbor 2.0 bin -neigh_modify delay 5 - -timestep 2.0 - -group peptide type <= 12 -group one id 2 4 5 6 -group two id 80 82 83 84 -group ref id 37 -group colvar union one two ref - -fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 - -fix 2 all plumed plumedfile plumed-restraint.dat outfile p.log -fix 2a ref setforce 0.0 0.0 0.0 - -fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 - -#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz -#dump_modify 1 sort id - -thermo_style custom step temp etotal pe ke epair ebond f_2 -thermo 10 -dump dd all xyz 10 lammps.xyz -variable step equal step -variable pe equal pe -fix 5 all print 10 "$(v_step) $(v_pe)" file lammps_energy -dump mq all custom 200 mq_lammps id mass q - -run 101 diff --git a/examples/USER/plumed/p.log b/examples/USER/plumed/p.log new file mode 100644 index 0000000000..79d0bbd84c --- /dev/null +++ b/examples/USER/plumed/p.log @@ -0,0 +1,57 @@ +PLUMED: PLUMED is starting +PLUMED: Version: 2.4.2 (git: Unknown) compiled on Jul 11 2018 at 19:09:03 +PLUMED: Please cite this paper when using PLUMED [1] +PLUMED: For further information see the PLUMED web page at http://www.plumed.org +PLUMED: Root: /Users/gareth/MD_code/lammps-permanent/lammps/lib/plumed/plumed2-2.4.2/ +PLUMED: For installed feature, see /Users/gareth/MD_code/lammps-permanent/lammps/lib/plumed/plumed2-2.4.2//src/config/config.txt +PLUMED: Molecular dynamics engine: LAMMPS +PLUMED: Precision of reals: 8 +PLUMED: Running over 1 node +PLUMED: Number of threads: 1 +PLUMED: Cache line size: 512 +PLUMED: Number of atoms: 2004 +PLUMED: File suffix: +PLUMED: FILE: plumed.dat +PLUMED: Action UNITS +PLUMED: with label @0 +PLUMED: length: A +PLUMED: energy: kcal/mol +PLUMED: time: ps +PLUMED: charge: e +PLUMED: mass: amu +PLUMED: using physical units +PLUMED: inside PLUMED, Boltzmann constant is 0.001987 +PLUMED: Action DISTANCE +PLUMED: with label dd +PLUMED: between atoms 45 48 +PLUMED: using periodic boundary conditions +PLUMED: Action RESTRAINT +PLUMED: with label @2 +PLUMED: with arguments dd +PLUMED: added component to this action: @2.bias +PLUMED: at 6.000000 +PLUMED: with harmonic force constant 2000.000000 +PLUMED: and linear force constant 0.000000 +PLUMED: added component to this action: @2.force2 +PLUMED: Action PRINT +PLUMED: with label @3 +PLUMED: with stride 1 +PLUMED: with arguments dd +PLUMED: on file colvar +PLUMED: with format %f +PLUMED: END FILE: plumed.dat +PLUMED: Timestep: 0.002000 +PLUMED: KbT has not been set by the MD engine +PLUMED: It should be set by hand where needed +PLUMED: Relevant bibliography: +PLUMED: [1] Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014) +PLUMED: Please read and cite where appropriate! +PLUMED: Finished setup +PLUMED: Cycles Total Average Minumum Maximum +PLUMED: 1 0.020354 0.020354 0.020354 0.020354 +PLUMED: 1 Prepare dependencies 102 0.000256 0.000003 0.000001 0.000006 +PLUMED: 2 Sharing data 102 0.010002 0.000098 0.000078 0.000546 +PLUMED: 3 Waiting for data 102 0.001398 0.000014 0.000011 0.000072 +PLUMED: 4 Calculating (forward loop) 102 0.001797 0.000018 0.000013 0.000058 +PLUMED: 5 Applying (backward loop) 102 0.002666 0.000026 0.000022 0.000062 +PLUMED: 6 Update 102 0.001126 0.000011 0.000007 0.000055 diff --git a/examples/USER/plumed/plumed-eng-ref.dat b/examples/USER/plumed/plumed-eng-ref.dat deleted file mode 100644 index 90e589157e..0000000000 --- a/examples/USER/plumed/plumed-eng-ref.dat +++ /dev/null @@ -1,2 +0,0 @@ -e: ENERGY -PRINT ARG=e FILE=energy_ref FMT=%8.4f diff --git a/examples/USER/plumed/plumed-engforce.dat b/examples/USER/plumed/plumed-engforce.dat deleted file mode 100644 index 31a1564798..0000000000 --- a/examples/USER/plumed/plumed-engforce.dat +++ /dev/null @@ -1,3 +0,0 @@ -e: ENERGY -RESTRAINT ARG=e AT=0 SLOPE=0.1 -PRINT ARG=e FILE=engforced FMT=%8.4f diff --git a/examples/USER/plumed/plumed-norestraint.dat b/examples/USER/plumed/plumed-norestraint.dat deleted file mode 100644 index 1fed74ae81..0000000000 --- a/examples/USER/plumed/plumed-norestraint.dat +++ /dev/null @@ -1,3 +0,0 @@ -UNITS LENGTH=A -dd: DISTANCE ATOMS=45,48 -PRINT ARG=dd FILE=lammps_restraint FMT=%8.4f diff --git a/examples/USER/plumed/plumed-restraint.dat b/examples/USER/plumed/plumed-restraint.dat deleted file mode 100644 index 6ae4c8ce10..0000000000 --- a/examples/USER/plumed/plumed-restraint.dat +++ /dev/null @@ -1,4 +0,0 @@ -UNITS LENGTH=A ENERGY=kcal/mol -dd: DISTANCE ATOMS=45,48 -RESTRAINT ARG=dd KAPPA=2000 AT=6.0 -PRINT ARG=dd FILE=plumed_restraint FMT=%8.4f diff --git a/examples/USER/plumed/plumed.dat b/examples/USER/plumed/plumed.dat index 7fe1290c0d..0437836d03 100644 --- a/examples/USER/plumed/plumed.dat +++ b/examples/USER/plumed/plumed.dat @@ -1,7 +1,4 @@ -UNITS ENERGY=kcal/mol -c1: COM ATOMS=2,4,5,6 -c2: COM ATOMS=80,82,83,84 -energy: ENERGY -DUMPATOMS ATOMS=1-2004 FILE=plumed.xyz UNITS=A PRECISION=4 STRIDE=10 -PRINT ARG=energy STRIDE=10 FMT=%8.4f FILE=plmd_energy -DUMPMASSCHARGE FILE=mq_plumed +UNITS LENGTH=A ENERGY=kcal/mol +dd: DISTANCE ATOMS=45,48 +RESTRAINT ARG=dd KAPPA=2000 AT=6.0 +PRINT ARG=dd FILE=colvar diff --git a/examples/USER/plumed/plumed_npt.dat b/examples/USER/plumed/plumed_npt.dat deleted file mode 100644 index 53579ac4ec..0000000000 --- a/examples/USER/plumed/plumed_npt.dat +++ /dev/null @@ -1,2 +0,0 @@ -vv: VOLUME -PRINT ARG=vv FILE=plmd_volume_without_restraint FMT=%8.5f diff --git a/examples/USER/plumed/plumed_npt2.dat b/examples/USER/plumed/plumed_npt2.dat deleted file mode 100644 index 2074128cd0..0000000000 --- a/examples/USER/plumed/plumed_npt2.dat +++ /dev/null @@ -1,3 +0,0 @@ -vv: VOLUME -RESTRAINT AT=0.0 ARG=vv SLOPE=-60.221429 -PRINT ARG=vv FILE=plmd_volume_with_restraint FMT=%8.5f