[lammps-users] will fix spring affect fix setforce 0 0 NULL output

HI, lammps users

I want to pull a silica sphere close to a membrane vertically using AFM.
so I used

fix AFM sio2 spring 700 0 0 ${z} 0
fix 1 sio2 setforce 0 0 NULL

what does f_1[z] means now?

Di Cheng

University of Science and Technology of China
Hefei, Anhui Province 230026
P. R. China
E-mail: [email protected]
Tel.: +86-15321055911

From the fix setforce doc page:

This fix computes a global 3-vector of forces, which can be accessed
by various output commands. This is the total force on the group of
atoms before the forces on individual atoms are changed by the fix.

The notation for the z-component would be f_1[3] - and it is the si02 group
of atoms before you zeroed it. Although with the NULL you didn't actually
change the z-force.

Steve

HI, lammps users

I want to pull a silica sphere close to a membrane vertically using AFM.
so I used

fix AFM sio2 spring 700 0 0 ${z} 0
fix 1 sio2 setforce 0 0 NULL

why don't you use "fix smd"?

it was written to deal with this
kind of scenario, i.e. pushing objects
around in a controlled way.

cheers,
   axel.

p.s.: if you want to do it in a more interactive and
less "controlled" way, watch out for an announcement
to the list later today.

Axel,

Thanks! I am trying fix smd. But here is my new problem:
It seems that the sio2 sphere is not moving with the R0.

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.
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

Axel,

Thanks! I am trying fix smd. But here is my new problem:
It seems that the sio2 sphere is not moving with the R0.

you are misunderstanding what R0 stands for.
you want r0 to be set to 0.0 and define your initial
Z value to be what the initial distance is going to be.

r0 is quite confusing and a legacy from fix spring
where r0 makes much more sense. it is slated to be
eliminated in a rewrite of the code which was started
last fall, but had to be postponed due to more urgent
projects requiring my attention.

cheers,
   axel.