Dear Sir,
I have used the following input scripts for my MD simulation. I didn’t get where I am doing time integration twice. Here is my input script for your consideration,
units real
boundary p p p
atom_style charge
read_data haslab_2.data
pair_style reax/c NULL safezone 3.0 mincap 400
pair_coeff * * CHONSMgPNaCuCl_v2.ff C H O N
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
variable b1 equal “time/25000000”
group HA id 1:505
group HA1 id 11:264
group HA2 id 281:495
group water id 506:14205
group firstHA id 1:10
group midHA id 265:280
group lastHA id 496:505
neighbor 5.0 bin
neigh_modify every 1 delay 0 one 10000
fix mynvt water nvt temp 300.0 300.0 250.0 #drag .01
fix nvt1 HA1 nvt temp 300.0 300.0 250.0
fix nvt3 midHA nvt temp 300.0 300.0 250.0
fix nvt2 HA2 nvt temp 300.0 300.0 250.0
fix 2 all qeq/reax 1000 0.0 10.0 1.0e-6 reax/c
fix 1 HA rigid group 2 firstHA lastHA
fix bonds all reax/c/bonds 1000 bonds.out
compute peratom all stress/atom NULL
fix moment1 HA momentum 1000 linear 1 0 1 angular
#fix moment2 midHA momentum 1000 linear 1 0 1 angular
fix moment3 lastHA momentum 1000 linear 1 0 1 angular
fix moment2 firstHA momentum 1000 linear 1 0 1 angular
fix 11 firstHA setforce 0.0 0.0 0.0
velocity firstHA set 0.0 0.0 0.0 rigid 1 units box
velocity lastHA set 0.0 NULL 0.0 rigid 1 units box
fix 22 lastHA setforce 0.0 0.0001 0.0
#velocity midHA set 0.0 NULL 0.0 rigid 1 units box
#fix 1st midHA setforce 0.0 NULL 0.0
fix last11 lastHA addforce 0.0 v_b1 0.0 every 1000
#compute displacement1 firstHA displace/atom
compute force lastHA property/atom fx fy fz
compute displacement2 lastHA displace/atom
dump myDump HA atom 1000 ha.lammpstrj
dump masterdump all custom 1000 master.lammpstrj id type q mass x y z vx vy vz c_peratom[1] c_peratom[2] c_peratom[3] c_peratom[4] c_peratom[5] c_peratom[6]
#dump first firstHA custom 1000 firstHA.lammpstrj id type q mass x y z c_displacement1[1] c_displacement1[2] c_displacement1[3] c_displacement1[4]
#dump last lastHA custom 1000 lastHA.lammpstrj id type q mass x y z c_displacement2[1] c_displacement2[2] c_displacement2[3] c_displacement2[4]
dump last lastHA custom 1000 lastHA.lammpstrj id type q mass xs ys zs c_displacement2[1] c_displacement2[2] c_displacement2[3] c_displacement2[4]
dump last1 lastHA custom 1000 lastHA1.lammpstrj id type q mass xs ys zs c_force[1] c_force[2] c_force[3]
timestep 0.25
thermo 1000
thermo_style custom step time temp press pxx pyy pzz pxy pxz pyz ke etotal enthalpy
run 150000
write_data haslab_3.data
#############################################run#########################################
Thank you. I am looking forward for your reply.
Best Regards,
Khandakar Abu Hasan Al Mahmud