Thanks for your reply. I have a simulation box that contains only water molecules. As you were said in previous mail I should use fix nve and fix langevin to bring this system to equilibrium then switch npt. I have written a script as below and used all numbers that including the interval [10,2000] and more with 50 steps for Tdamp and Pdamp. Also, [0.2,2] for drag. But the system was not balanced(water have created by VMD). would you help me?
#TIP3P water model
units real
neigh_modify delay 2 every 1
atom_style full
bond_style harmonic
angle_style charmm
pair_style lj/charmm/coul/long 9 10
kspace_style pppm 1e-4
read_data solvate.data
pair_coeff 1 1 0.046 0.4000135 0.046 0.4000135 # H
pair_coeff 2 2 0.1521 3.150574 0.1521 3.150574 # O
pair_coeff 1 2 0.0836 1.7753 0.0836 1.7753 # O-H
minimize 1e-10 1e-16 100000 1000000
special_bonds charmm
fix 1 all nve
fix 2 all shake 1e-6 500 0 m 1.0 a 1
fix 3 all langevin 300.0 300.0 400 655465
velocity all create 300.0 12345678 dist uniform
thermo 100
thermo_style custom step temp press vol ke
timestep 0.5
run 400000
unfix 1
unfix 3
fix 4 all npt 300.0 300.0 200 xyz 1 1 1000.0 drag 0.2
run 1000000
Many thanks,
Yasti
Thanks for your reply. I have a simulation box that contains only water
molecules. As you were said in previous mail I should use fix nve and fix
langevin to bring this system to equilibrium then switch npt. I have written
a script as below and used all numbers that including the interval
[10,2000] and more with 50 steps for Tdamp and Pdamp. Also, [0.2,2] for
drag. But the system was not balanced(water have created by VMD). would you
help me?
i have two remarks to this.
a) i don't really understand what you are asking for. and
b) please keep in mind that this list of not "steve and the gang's
school of md",
i.e. please don't just dump an input script on us and say "it doesn't work,
please help me to fix it". this means that i am happy to give my personal
opinion on what is a good strategy to equilibrate an input, it is your job to
teach yourself what the various options mean in practice.
in general, you should always consider to make it as easy as possible
to give and answer. for example, "the system was not balanced" doesn't
tell me anything. if you would write: i want to do XXX, and in order to achive
this i did YYY and then ZZZ. i expected to see AAA, but instead something
else happened. then it would usually be easy to answer and you would get
(some) help or some kind of suggestion that should point you into the right
direction. sometimes it is useful to include the input script, especially if you
have reason to assume that your problem is related to your input not
enabling the functionality in lammps that you want to use. but if the problem
would be in how you set up your model, then it is near impossible to give an
from just having a look at the input. if that would be possible, then you don't
have to do a simulation anymore.
the situation is different, however, if you believe that you have found a
bug in the code. in this case it is highly recommended to provide a
_complete_ set of files that reproduces the bug. the only stipulation
would be that you make every attempt to generate an input that is as
small as possible and still shows the problem.
i hope that explains matters a bit.
cheers,
axel.