Dear Trung,
When i substitute rigid/nvt/small for rigid/npt/small(rigid/npt) as follow, NaNs similarly show
©fix 1 RIGID rigid/nvt/small molecule temp 300 300 5
©result
Step thermo Dt f_1 rigid_temp rigid_ke rigid_rot
0 284.90993 1 7077.3253 243.63538 2720.3939 1636.5375
1000 nan 1 -nan nan nan nan
2000 nan 1 -nan nan nan nan
3000 nan 1 -nan nan nan nan
4000 nan 1 -nan nan nan nan
5000 nan 1 -nan nan nan nan
What happens for using rigid/npt and rigid/nvt?
I paste a simple case as follow ,(with case (A)rigid/nve/small, (B)rigid/npt/small,©rigid/nvt/small.)
units real
boundary p p p
atom_style hybrid ellipsoid molecular
lattice sc 50
region box block 0 10 0 10 0 10
create_box 2 box
create_atoms 1 single 250 250 250 units box
create_atoms 1 single 100 100 100 units box
create_atoms 2 single 268 250 250 units box #250+16.5+1.5=268 #3
create_atoms 2 single 118 100 100 units box #100+16.5+1.5=118 #4
mass 1 1020.29
set type 1 shape 33.0 16.0 3.5
mass 2 0.1
set type 2 shape 3.0 3.0 3.0
set atom 1 mol 1
set atom 3 mol 1
set atom 2 mol 2
set atom 4 mol 2
group GB type 1
group ghost type 2
pair_style hybrid/overlay gayberne 1 1 1 40.0
pair_coeff 1 1 gayberne 0.1 1.75 2 2 10 0 0 0
pair_coeff 1 2 gayberne 0.00001 3.0 1 1 1 0 0 0
pair_coeff 2 2 gayberne 0.00001 3.0 1 1 1 0 0 0
neighbor 2.0 bin
timestep 1
thermo 1000
compute thermo all temp/asphere
thermo_modify temp thermo
group RIGID molecule 1:2
compute RIGID RIGID temp
velocity all create 300.0 333
#(A)NVE------------------------
fix 1 RIGID rigid/nve/small molecule langevin 300.0 300.0 10.0 2211
fix 11 ghost nve
fix 12 ghost langevin 300.0 300 10.0 2133
fix 4 RIGID dt/reset 10 0.01 5.0 0.02 units box
#(B)NPT-------------NaN----------
#fix 1 RIGID rigid/npt/small molecule temp 300.0 300.0 10.0 iso 10 10 10
#fix_modify 1 temp thermo
#fix 4 RIGID dt/reset 10 0.01 5.0 0.02 units box
#©NVT--------------NaN----------
#fix 1 RIGID rigid/nvt/small molecule temp 300.0 300.0 10.0
#fix 4 RIGID dt/reset 10 0.01 5.0 0.02 units box
compute rigid_ke RIGID ke/rigid 1
compute rigid_rot RIGID erotate/rigid 1
variable total_ke equal “c_rigid_ke+c_rigid_rot”
variable dof equal 62
variable boltz equal 1.987e-3
variable rigid_temp equal "2.0v_total_ke/v_dof/v_boltz"
thermo_style custom step c_thermo dt f_1 v_rigid_temp c_rigid_ke c_rigid_rot pe