Hello all,
Following is the input file I created to run a minimization, nvt and npt for the peptide in the lammps examples section.
units real
neigh_modify delay 2 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8 10
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.peptide
special_bonds charmm
min_style cg #This is the default. Indicated for clarity.
minimize 1.0e-4 100 1000
thermo 1
thermo_style multi
timestep 1
restart 10 dataminim.restart1 dataminim.restart2
dump 1 all atom 10 dataminim.dump
dump_modify 1 image yes scale yes
End of Minimization. Begining NVT
fix 1 all nvt 275.0 275.0 100.0
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
velocity all create 0.0 12345678 dist uniform
thermo 100
thermo_style multi
timestep 1
restart 10 datanvt.restart1 datanvt.restart2
dump 2 all atom 10 datanvt.dump
dump_modify 2 image yes scale yes
run 10000
End of NVT. Begining NPT
fix 3 all npt 275.0 275.0 100.0 xyz 1.0 1.0 1000.0 #Performing a NPT simulation with an isotropic pressure of 1atm.
thermo 1
thermo_style multi
timestep 1
restart 10 datanpt.restart1 datanpt.restart2
dump 3 all atom 10 datanpt.dump
dump_modify 3 image yes scale yes
run 20
Following is the output I got…
PPPM initialization …
G vector = 0.268725
grid = 15 15 15
RMS precision = 4.85953e-05
brick FFT buffer size/proc = 10648 3375 5808
Memory usage per processor = 19.8619 Mbytes
Step Temp E_pair E_mol TotEng Press
0 190.08718 -6442.7656 70.391457 -5237.4557 20368.349
96 190.08718 -8644.3786 499.33865 -7010.1215 20368.349
Loop time of 33.2691 on 1 procs for 100 steps with 2004 atoms
Minimization stats:
E initial, next-to-last, final = -6372.37 -8144.41 -8145.04
Gradient 2-norm init/final= 1059.36 30.2441
Gradient inf-norm init/final= 58.6026 9.45785
Iterations = 96
Force evaluations = 353
.
.
.
---------------- Step 100 ----- CPU = 0.4142 (sec) ----------------
TotEng = -7683.1056 KinEng = 0.9780 Temp = 0.2431
PotEng = -7684.0836 E_bond = 5.3974 E_angle = 8.5483
E_dihed = 10.5501 E_impro = 0.0872 E_vdwl = 1006.8575
E_coul = 25203.7728 E_long = -33919.2969 Press = -3548.1608
SHAKE stats (type/ave/delta) on step 200
4 1.111 4.22323e-07
6 0.997 5.9652e-08
8 1.08 4.14227e-08
10 1.111 1.50259e-08
12 1.08 3.33095e-08
14 0.96 0
18 0.9572 1.37e-06
31 104.52 0.000103274
.
.
.
---------------- Step 10099 ----- CPU = 0.3181 (sec) ----------------
TotEng = -5314.6396 KinEng = 1143.1326 Temp = 284.1445
PotEng = -6457.7722 E_bond = 14.0841 E_angle = 20.4752
E_dihed = 14.2131 E_impro = 0.8314 E_vdwl = 644.2920
E_coul = 26753.3137 E_long = -33904.9818 Press = -19546.5594
Volume = 20506.3172
SHAKE stats (type/ave/delta) on step 10100
4 1.10657 0.0177904
6 0.988234 0.0129708
8 1.07508 0.0131734
10 1.10905 0.0127183
12 1.0756 0.011401
14 0.956341 0
18 0.945594 0.112877
31 104.789 11.3552
---------------- Step 10100 ----- CPU = 0.5103 (sec) ----------------
TotEng = -4515.9580 KinEng = 1647.1192 Temp = 409.4187
PotEng = -6163.0771 E_bond = 14.7211 E_angle = 21.4911
E_dihed = 14.1678 E_impro = 1.0336 E_vdwl = 639.7163
E_coul = 27052.3297 E_long = -33906.5367 Press = 62704.5703
Volume = 20505.9821
---------------- Step 10101 ----- CPU = 0.6695 (sec) ----------------
TotEng = 517.7304 KinEng = 7731.9595 Temp = 1921.9062
PotEng = -7214.2292 E_bond = 16.4958 E_angle = 23.8416
E_dihed = 14.4167 E_impro = 1.4070 E_vdwl = 671.1836
E_coul = 25959.3555 E_long = -33900.9294 Press = -249024.8820
Volume = 20506.7001
---------------- Step 10102 ----- CPU = 0.8749 (sec) ----------------
TotEng = nan KinEng = nan Temp = nan
PotEng = -3837.9466 E_bond = 19.8407 E_angle = 26.4321
E_dihed = 14.7870 E_impro = 1.6216 E_vdwl = 630.8032
E_coul = 29364.8711 E_long = -33896.3023 Press = nan
Volume = 20503.2360
ERROR: Out of range atoms - cannot compute PPPM