use command fix smd to calculate pmf

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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