Dear Lammps users,
I am calculating the PMF of two atoms in a 161616 box. Atomic information is stored in data file. There are 4096 atoms in my box. I used fix smd command to calculate the PMF. The initial distance between atoms is 2.7. But the result showed that the distance between the two atoms was 184. After I changed the atoms’ number. But the results are same. I am confused about the result. I apologize in advance if the question is stupid but any suggestions would be appreciable.
The input file is showed below.
variable t equal 0.6
variable rc equal 5.0
problem setup
units lj
atom_style atomic
neigh_modify delay 0 every 1
pair_style lj/cut ${rc}
read_data data.second
pair_coeff * * 1 1
mass * 1.0
group 1 id 3550
group 2 id 1916
0 minize
thermo 100000
thermo_style custom step temp press vol etotal pe cpuremain
min_style cg
minimize 1e-6 1e-10 10000 100000
write_restart cg.restart
NPT run
timestep 0.003
fix 1 all nvt temp $t $t 0.5
compute F 1 reduce sum fx fy fz
fix F 1 ave/time 1 1000 1000 c_F[1] c_F[2] c_F[3] ave one file Force.txt
compute msd 1 msd
fix msd 1 ave/time 1 1000 1000 c_msd[2] ave one file MSD.txt
thermo 1000
thermo_style custom step temp pe etotal vol c_F[1] c_F[2] c_F[3] cpuremain
thermo_modify flush yes
fix pull 1 smd cvel 5 -0.1 couple 2 auto auto auto 0.0
fix force 1 ave/time 1 10 10 f_pull[1] f_pull[2] f_pull[3] f_pull[4] f_pull[5] f_pull[6] f_pull[7] ave one file PMF.txt
dump 2 all custom 100 nvt2.lammpstrj id type element x y z
dump_modify 2 element C sort id
run 500000
Thank you for your help.
Best Regards,
Gerry Wong
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