Hi, Axel

I am still confused about what happened in fix smd. You said:

consider that you have a spring and a (strong) wire. the length

of the wire is R0. your group is connected to this wire and the

spring which is then connected to your reference point. the wire

always keeps the moving part of the spring at a distance of R0

from your group. this makes sense for fix spring, but not in

steered MD.

When R0 is set to be zero, the model is simplified like this:

sio2---spring---ref.point

>______________|

>

R

Now I use constant velocity mode, set velocity to be 1.0. Which end of

the spring is moving, sio2 end or ref.point end?

#logout:

LAMMPS (18 Apr 2010)

# Created by charmm2lammps v1.8.1 on Sun Apr 4 20:05:41 CST 2010

boundary p p p

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

Scanning data file ...

4 = max bonds/atom

6 = max angles/atom

18 = max dihedrals/atom

1 = max impropers/atom

Reading data file ...

orthogonal box = (-24 -24 -33.6931) to (24 24 83.5)

1 by 1 by 1 processor grid

27324 atoms

27324 velocities

21428 bonds

24562 angles

31944 dihedrals

144 impropers

Finding 1-2 1-3 1-4 neighbors ...

4 = max # of 1-2 neighbors

12 = max # of 1-3 neighbors

16 = max # of 1-4 neighbors

20 = max # of special neighbors

special_bonds charmm

#define groups

group sio2 type 17 18 19 20 21

354 atoms in group sio2

group water type 2 13

17610 atoms in group water

group other subtract all sio2

26970 atoms in group other

group lipid subtract other water

9360 atoms in group lipid

region lower block -INF INF -INF INF -INF -15 units box

group lower region lower

4526 atoms in group lower

group lower_lipid intersect lower lipid

1201 atoms in group 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

Finding SHAKE clusters ...

0 = # of size 2 clusters

0 = # of size 3 clusters

0 = # of size 4 clusters

5870 = # of frozen angles

fix rigid sio2 rigid molecule

1 rigid bodies with 354 atoms

# hold lower lipid bilayer

fix hold_lipid lower_lipid spring/self 10

# pull

fix pull sio2 smd cvel 50 -0.001 tether NULL NULL 37 0

# fix 2_sio2 sio2 nve

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

# fix all

# generate initial velocity

velocity other create 323.15 1468 dist uniform

velocity sio2 set 0 0 -0.001 units box

thermo 10

thermo_style custom step cpu temp press f_pull[3] f_pull[4]

f_pull[5] f_pull[6] f_pull[7]

# 1fs per step

timestep 1

dump 1 all atom 10 dump.dppc.addH.xx

run 200000

Setting up run ...

Memory usage per processor = 105.505 Mbytes

Step CPU Temp Press pull[3] pull[4] pull[5] pull[6] pull[7]

0 0 323.2253 1.0353196e+15 3.5527137e-13

-3.5527137e-13 5.8980485 5.8996228 -3.5527137e-16

10 4.697108 1206.4801 -1.2635928e+15 0.032503132

-0.032503132 5.8880485 5.8889738 -0.00012854972

20 9.5625679 nan nan -1.0421669e-316

1.0421669e-316 5.8780485 nan -0.00072789367

30 10.417853 nan nan -1.0421669e-316

1.0421669e-316 5.8680485 nan -0.00072789367

40 11.277054 nan nan -1.0421669e-316

1.0421669e-316 5.8580485 nan -0.00072789367

50 12.133108 nan nan -1.0421669e-316

1.0421669e-316 5.8480485 nan -0.00072789367

60 12.990315 nan nan -1.0421669e-316

1.0421669e-316 5.8380485 nan -0.00072789367

70 13.847533 nan nan -1.0421669e-316

1.0421669e-316 5.8280485 nan -0.00072789367

80 14.706971 nan nan -1.0421669e-316

1.0421669e-316 5.8180485 nan -0.00072789367

90 15.563443 nan nan -1.0421669e-316

1.0421669e-316 5.8080485 nan -0.00072789367

100 16.418641 nan nan -1.0421669e-316

1.0421669e-316 5.7980485 nan -0.00072789367

Di Cheng

University of Science and Technology of China

Hefei, Anhui Province 230026

P. R. China

E-mail: [email protected]...

Tel.: +86-15321055911