HI,lammps-users
I am trying fix smd to pull my silica sphere. But the problem is:It
seems that the sio2 sphere is not moving with the R0.
I am using lammps-18Apr10
the data.test is converted from a restart file. which placed the sio2
sphere at 0 0 37, and the lipid bilayer is at x-y plane
here is my in.script
# Created by charmm2lammps v1.8.1 on Sun Apr 4 20:05:41 CST 2010
boundary p p p# p p m with wall/reflect failed. not solved
units real
neigh_modify delay 2 every 1
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
#kspace_style pppm 1e-4
read_data data.test
special_bonds charmm
#define groups
group sio2 type 17 18 19 20 21
group water type 2 13
group other subtract all sio2
group lipid subtract other water
region lower block -INF INF -INF INF -INF -15 units box
group lower region lower
group lower_lipid intersect lower lipid
#minimize
#minimize 1.0e-10 1.0e-12 100 1000
# fix nvt on water and lipid
fix 1 other nvt temp 323.15 323.15 100
# fix all tip3p water model
fix 2 water shake 1e-6 500 0 b 17 a 31
fix pull sio2 smd cvel 10000 -0.001 tether NULL NULL 0 37
#fix 2_sio2 sio2 nve/noforce
#fix sio2 sio2 setforce 0 0 NULL
#compute sio2 sio2 reduce sum fz
# output forces acted upon sio2 sphere
fix f_sio2 sio2 ave/time 1 500 1000 f_pull[3] f_pull[4]
f_pull[5] f_pull[6] f_pull[7] file f_sio2.addH.xx #1 indicates 1m/s =
0.01A/ps
# fix all
# hold lower lipid bilayer
fix hold_lipid lower_lipid spring/self 10
# generate initial velocity
velocity other create 323.15 1245678 dist uniform
velocity sio2 set 0 0 -0.001 units box
thermo 100
thermo_style custom step cpu temp press pe ke etotal f_pull[3]
f_pull[4] f_pull[5] f_pull[6] f_pull[7]
# 1fs per step
timestep 1
dump 1 all atom 1000 dump.dppc.addH.xx
run 200000