Loading examples/USER/plumed/check-plumed.sh +49 −0 Original line number Diff line number Diff line #!/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 Loading Loading @@ -30,3 +35,47 @@ if [ "$nlines" -gt 0 ] ; then 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 # Nothing from here works # Now try to simply increase the size of the box by applying a moving restraint on the volume $LAMMPS < in.peptide-plumed-expand # Now run calculations to test virial $LAMMPS < in.peptide-plumed-npt $LAMMPS < in.peptide-plumed-npt2 # Now run calculations to check forces on energy $LAMMPS < in.peptide-plumed-engforce-ref $LAMMPS < in.peptide-plumed-eng-force-plumed examples/USER/plumed/clear-files.sh 0 → 100755 +8 −0 Original line number Diff line number Diff line #!/bin/bash # Data from first set of checks rm bck.* plmd_energy lammps_energy mq_plumed mq_lammps lammps.xyz plumed.xyz p.log # Data from checks on restraints rm bck.* p.log lammps_restraint plumed_restraint # Data from checks on virial rm bck.* lammps_energy lammps.xyz log.lammps plmd_volume p.log plmd_volume_without_restraint plmd_volume_with_restraint examples/USER/plumed/in.peptide-plumed +1 −0 Original line number Diff line number Diff line Loading @@ -39,5 +39,6 @@ dump dd all xyz 10 lammps.xyz variable step equal step variable pe equal pe fix 5 all print 10 "$(v_step) $(v_pe)" file lammps_energy dump mq all custom 200 mq_lammps id mass q run 101 examples/USER/plumed/in.peptide-plumed-eng-force-plumed 0 → 100644 +41 −0 Original line number Diff line number Diff line # Solvated 5-mer peptide units real atom_style full pair_style lj/charmm/coul/long 8.0 10.0 10.0 bond_style harmonic angle_style charmm dihedral_style charmm improper_style harmonic kspace_style pppm 0.0001 read_data data.peptide neighbor 2.0 bin neigh_modify delay 5 timestep 1.8181818181818181 group peptide type <= 12 group one id 2 4 5 6 group two id 80 82 83 84 group ref id 37 group colvar union one two ref fix 1 all nvt temp 363.0 363.0 90.90909090909091 tchain 1 fix 2 all plumed plumedfile plumed-engforce.dat outfile p.log #dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz #dump_modify 1 sort id thermo_style custom step temp etotal pe ke epair ebond f_2 thermo 10 dump dd all xyz 10 lammps.xyz variable step equal step variable pe equal pe fix 5 all print 10 "$(v_step) $(v_pe)" file lammps_energy dump mq all custom 200 mq_lammps id mass q run 101 examples/USER/plumed/in.peptide-plumed-engforce-ref 0 → 100644 +40 −0 Original line number Diff line number Diff line # 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 Loading
examples/USER/plumed/check-plumed.sh +49 −0 Original line number Diff line number Diff line #!/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 Loading Loading @@ -30,3 +35,47 @@ if [ "$nlines" -gt 0 ] ; then 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 # Nothing from here works # Now try to simply increase the size of the box by applying a moving restraint on the volume $LAMMPS < in.peptide-plumed-expand # Now run calculations to test virial $LAMMPS < in.peptide-plumed-npt $LAMMPS < in.peptide-plumed-npt2 # Now run calculations to check forces on energy $LAMMPS < in.peptide-plumed-engforce-ref $LAMMPS < in.peptide-plumed-eng-force-plumed
examples/USER/plumed/clear-files.sh 0 → 100755 +8 −0 Original line number Diff line number Diff line #!/bin/bash # Data from first set of checks rm bck.* plmd_energy lammps_energy mq_plumed mq_lammps lammps.xyz plumed.xyz p.log # Data from checks on restraints rm bck.* p.log lammps_restraint plumed_restraint # Data from checks on virial rm bck.* lammps_energy lammps.xyz log.lammps plmd_volume p.log plmd_volume_without_restraint plmd_volume_with_restraint
examples/USER/plumed/in.peptide-plumed +1 −0 Original line number Diff line number Diff line Loading @@ -39,5 +39,6 @@ dump dd all xyz 10 lammps.xyz variable step equal step variable pe equal pe fix 5 all print 10 "$(v_step) $(v_pe)" file lammps_energy dump mq all custom 200 mq_lammps id mass q run 101
examples/USER/plumed/in.peptide-plumed-eng-force-plumed 0 → 100644 +41 −0 Original line number Diff line number Diff line # Solvated 5-mer peptide units real atom_style full pair_style lj/charmm/coul/long 8.0 10.0 10.0 bond_style harmonic angle_style charmm dihedral_style charmm improper_style harmonic kspace_style pppm 0.0001 read_data data.peptide neighbor 2.0 bin neigh_modify delay 5 timestep 1.8181818181818181 group peptide type <= 12 group one id 2 4 5 6 group two id 80 82 83 84 group ref id 37 group colvar union one two ref fix 1 all nvt temp 363.0 363.0 90.90909090909091 tchain 1 fix 2 all plumed plumedfile plumed-engforce.dat outfile p.log #dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz #dump_modify 1 sort id thermo_style custom step temp etotal pe ke epair ebond f_2 thermo 10 dump dd all xyz 10 lammps.xyz variable step equal step variable pe equal pe fix 5 all print 10 "$(v_step) $(v_pe)" file lammps_energy dump mq all custom 200 mq_lammps id mass q run 101
examples/USER/plumed/in.peptide-plumed-engforce-ref 0 → 100644 +40 −0 Original line number Diff line number Diff line # 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
