Dear LAMMPS-users
I am trying to use fix smd for a protein - DNA assembly system using LAMMPS/15May2015. I want to calculate the PMF for the case when protein is being pulled between two almost parallel DNA walls. I used the command as described in the manual.
fix 7 pull smd cvel 5.0 -0.001 tether NULL 150.0 NULL 0.0
where pull is the group-id for alpha-C (atom type 11) of amino acids. However when I visualized my results in VMD, I observe that the whole system (DNA + protein) is moving instead of protein only. I double checked that type 11 only belongs to protein molecule. I also ran with force constants 50 and 500. But the behavior is identical. The whole system is immersed in a box of water molecules with counter-ions present to neutralize the charge. Can you please provide some suggestions where I am making a mistake. I have also attached the input script below.
units real
neigh_modify delay 2 every 1
boundary p p p
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/charmm 8 10
pair_modify mix arithmetic
read_restart Origami_new_thrombin_v08_wb_ions.restart7
group origami type 1:3 5:32 34:73
group protein id <> 71228 75706
group pull type 11 # alpha-C of amino acids
special_bonds charmm
fix 7 pull smd cvel 5.0 -0.001 tether NULL 150.0 NULL 0.0
thermo 1000
thermo_style custom step temp ke pe etotal enthalpy f_7[5] f_7[6] f_7[7]
timestep 0.5
restart 10 Origami_new_thrombin_v08_wb_ions.restart9 Origami_new_thrombin_v08_wb_ions.restart10
fix 1 all shake 1e-6 500 0 m 1.008 a 245 b 125
dump 4 all custom 2000 Origami_new_thrombin_v08_wb_ions_11.dump id type x y z
fix 3 all nvt temp 300 300 50
run 200000
undump 4
unfix 3
unfix 7
unfix 1
Kind Regards
Narendra