Dear Lammps Users and Developers,
i am working on ssDNA and CNT simulations.in my cofiguration cnt is freezed in the center of my simulation box and ssDNA is a few angstrom away from cnt.and i am keeping the temperature at 300 K with conanical enseble on ssDNA and ions.and velocity is 300 Angstroms/femtosecond on ssDNA and ions.
commands in my input script:
fix 1 nagt1 nvt temp 400.0 400.0 100.0
velocity nagt1 create 300.0 4928459 dist gaussian
after i made my simulation i see in thermodynamic data output of the temperature :
0.281547 K and it is getting lower and lower.when i visualize my system with vmd i can see that my ssDNA is not moving.
i used this configuration and the commends for thy sequenced ssDNA and it worked fine.when i changed the sequence to thy-gua i faced with this problem. what might cause to this problem?
part of my input file:
units real
neigh_modify delay 2 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
kspace_style pppm 1.0e-4
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
read_data cnt-gt1.data
pair_coeff 1 1 0.07 3.55
pair_coeff 2 2 0.046 0.4000135
pair_coeff 3 3 0.046 0.4000135
pair_coeff 4 4 0.046 1.959977
pair_coeff 5 5 0.046 0.4000135
pair_coeff 6 6 0.022 2.351973
pair_coeff 7 7 0.028 2.387609
pair_coeff 8 8 0.024 2.387609
pair_coeff 9 9 0.1 3.385415
pair_coeff 10 10 0.1 3.385415
pair_coeff 11 11 0.1 3.385415
pair_coeff 12 12 0.09 3.385415
pair_coeff 13 13 0.09 3.385415
pair_coeff 14 14 0.075 3.385415
pair_coeff 15 15 0.075 3.385415
pair_coeff 16 16 0.075 3.385415
pair_coeff 17 17 0.01 3.385415
pair_coeff 18 18 0.01 3.385415
pair_coeff 19 19 0.01 3.385415
pair_coeff 20 20 0.01 3.385415
pair_coeff 21 21 0.2 3.296325
pair_coeff 22 22 0.2 3.296325
pair_coeff 23 23 0.2 3.296325
pair_coeff 24 24 0.2 3.296325
pair_coeff 25 25 0.2 3.296325
pair_coeff 26 26 0.2 3.296325
pair_coeff 27 27 0.12 3.029056
pair_coeff 28 28 0.1521 3.153781
pair_coeff 29 29 0.12 3.029056
pair_coeff 30 30 0.1521 3.153781
pair_coeff 31 31 0.1521 3.153781
pair_coeff 32 32 0.585 3.830864
pair_coeff 33 33 0.0469 2.429926
group cnt type 1
group gt1 type <> 2 32
group nagt1 type <> 2 33
group all type <> 1 33
timestep 0.5
turns off the pairwise interaction in cnt
neigh_modify exclude molecule cnt
#carries the cnt to center of box
fix tocenter cnt recenter 0.0 0.0 0.0 units box
unfix tocenter
displace_atoms nagt1 move 0.0 7.0 0.0 units box
#freeze the cnt
fix freeze cnt setforce 0.0 0.0 0.0
#holding the temperature at 300 K
fix 1 nagt1 nvt temp 400.0 400.0 100.0
velocity nagt1 create 300.0 4928459 dist gaussian
…
thanks,
Aysun Itai