Dear Users
I want to simulate some examples that are in the lammps directory, but i encountered with
these problems, i use linux os and lmp_serial:
ali-pc@…3859…:~/md/lammps-28Oct12/examples/micelle$ /home/ali-pc/md/lammps-28Oct12/src/lmp_serial<in.micelle
LAMMPS (28 Oct 2012)
Scanning data file …
1 = max bonds/atom
Reading data file …
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
1 by 1 by 1 MPI processor grid
1200 atoms
300 bonds
Finding 1-2 1-3 1-4 neighbors …
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
Finding 1-2 1-3 1-4 neighbors …
2 = max # of 1-2 neighbors
2 = max # of special neighbors
ERROR: Illegal fix nvt/npt/nph command (fix_nh.cpp:54)
What was the fix npt/nph/nvt that you used in your .inp file. You should take a look at that and compare it to manual you are probably missing something.
Dear Yasaman
I am a newcomer in LAMMPS and i want to simulate its examples, micelle example,
Its in. file:
2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
Soft potential push-off
read_data data.micelle
special_bonds fene
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nvt
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
unfix 3
Main run
pair_style lj/cut 2.5
solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
#dump 1 all atom 2000 dump.micelle
#dump 1 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
run 60000
Dear Yasaman
I am a newcomer in LAMMPS and i want to simulate its examples, micelle
example,
Its in. file:
no. this is a modified input.
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
special_bonds fene
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nvt
but the micelle example has "fix 1 all nve" at this location...
using "fix 1 all nvt" without any arguments is *wrong*
exactly as the error message says.
axel.
Dear Ali,
Here is an example of fix nvt from manual
fix 1 all nvt temp 300.0 300.0 100.0
You need to specify temperature as well as damping factor.
Make sure that you read manual very carefully and pay attention to it's examples.
Dear Ali,
Here is an example of fix nvt from manual
fix 1 all nvt temp 300.0 300.0 100.0
You need to specify temperature as well as damping factor.
Make sure that you read manual very carefully and pay attention to it's
examples.
....and particularly the fact, that one must not use fix nvt
(or npt) in combination with any other method of thermalization,
e.g. fix temp/rescale.
please also note, that the examples in the example directory
are not meant to teach how to do "good MD", but rather showcase
specific features. in many cases, they take shortcuts that are
ok for demonstration purposes, but are not a good idea for a
proper MD where you want to get useful statistical mechanical data.
(the use of temp/rescale is an example for such a shortcut that
is not a good idea in 99% of "normal" MD runs).
axel.
Dear users
Thank you for your reply dear Yasaman and Axel,
Dear All,
I am new to LAMMPS and I am wanting to simulate a lipid bilayer using the CMM lipids (from Mike Klein and co-workers) in LAMMPS.
Is there a tutorial online somewhere? I have looked, but couldn't find any.
Best regards,
Jesper
Dear All,
I am new to LAMMPS and I am wanting to simulate a lipid bilayer using the CMM lipids (from Mike Klein and co-workers) in LAMMPS.
Is there a tutorial online somewhere? I have looked, but couldn't find any.
tutorial for doing what?
you can use the coarse grain model very much like
any other force field for molecular simulations.
is there any specific problem that you are running into?
axel.