diff --git a/examples/PACKAGES/pimd/para-h2/in.scp b/examples/PACKAGES/pimd/para-h2/in.scp index bee3a6e081..eb8debad15 100644 --- a/examples/PACKAGES/pimd/para-h2/in.scp +++ b/examples/PACKAGES/pimd/para-h2/in.scp @@ -15,13 +15,14 @@ pair_coeff 1 * pair.table PAIR_H2 timestep 0.001 -thermo_style custom step temp pe etotal pzz -thermo ${out_freq} - velocity all create 1.0 1985 rot yes dist gaussian fix 1 all pimd method nmpimd fmass 1.0 temp 25.0 nhc 4 +thermo_style custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3] +thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial +thermo ${out_freq} + #dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd #restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2 diff --git a/examples/PACKAGES/pimd/para-h2/run.sh b/examples/PACKAGES/pimd/para-h2/run.sh index ace20f84ea..5304db5917 100644 --- a/examples/PACKAGES/pimd/para-h2/run.sh +++ b/examples/PACKAGES/pimd/para-h2/run.sh @@ -1 +1 @@ -mpirun -np 64 lmp_mpi -partition 8x8 -in in.scp -log logfile/log.lammps -screen screen/screen +mpirun -np 64 lmp_mpi -partition 8x8 -in in.scp -log log.lammps -screen none diff --git a/examples/PACKAGES/pimd/prot-hairpin/in.scp b/examples/PACKAGES/pimd/prot-hairpin/in.scp index 220d29dc51..00b5150a8a 100644 --- a/examples/PACKAGES/pimd/prot-hairpin/in.scp +++ b/examples/PACKAGES/pimd/prot-hairpin/in.scp @@ -14,18 +14,19 @@ pair_modify mix arithmetic kspace_style pppm 1e-4 read_data system.data -#read_restart restart/system_${ibead}.rest1 +#read_restart system_${ibead}.rest1 special_bonds charmm fix 1 all pimd method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0 thermo 10 -thermo_style custom step temp pe etotal +thermo_style custom step temp pe etotal f_1[1] f_1[2] f_1[3] +thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial timestep 0.08 -restart 100 restart/system_${ibead}.rest1 restart/system_${ibead}.rest2 +# restart 100 system_${ibead}.rest1 system_${ibead}.rest2 group prot id <= 256 -dump 1 prot dcd 100 dcd/prot_${ibead}.dcd +# dump 1 prot dcd 100 prot_${ibead}.dcd -run 2000000 +run 200 diff --git a/examples/PACKAGES/pimd/prot-hairpin/run.sh b/examples/PACKAGES/pimd/prot-hairpin/run.sh index 1423960325..756cc14461 100644 --- a/examples/PACKAGES/pimd/prot-hairpin/run.sh +++ b/examples/PACKAGES/pimd/prot-hairpin/run.sh @@ -1 +1 @@ -mpirun -np 8 lmp_mpi -partition 8x1 -in in.scp -log logfile/log.lammps -screen screen/screen +mpirun -np 8 lmp_mpi -partition 8x1 -in in.scp -log log.lammps -screen none