Hello Lammps Users,
I am trying to run a nvt simulation of CO2. I was told that I could use a combination of
fix nve and fix temp/berendsen to do so.
But I keep obtaining negative pressures. I don’t know what I need to change to not get negative pressures anymore. If I use fix nvt, I also get negative pressures.
Also, I would like to know why some molecules have atoms missing, for example it is supposed to have 1 carbon and 2 oxygen per molecule, but sometimes it gets only 1 carbon and 1 oxygen. (I uploaded a image, so you can see this). And what I can do to fix this molecule thing.
I am using Lammps version 16Aug13.
My input code and my log file are attached.
Thank you,
data3.co2 (7.98 KB)
in.co2 (942 Bytes)
log.lammps (6.3 KB)
Hello Lammps Users,
I am trying to run a nvt simulation of CO2. I was told that I could use a
combination of
fix nve and fix temp/berendsen to do so.
But I keep obtaining negative pressures. I don't know what I need to change
to not get negative pressures anymore. If I use fix nvt, I also get negative
pressures.
have you discussed this with your supervisor? your question indicates
that you need some more background knowledge in MD simulations and
statistical mechanics and thermodynamics. there is no point in asking
to make something go away when you don't understand why it is there in
the first place (and in your case legitimately so).
please note that what you are seeing in the output is instantaneous
pressure and that pressure will fluctuate. a lot...
you are not the first person asking about this, so please see the
mailing list archive about previous discussion on the subject.
Also, I would like to know why some molecules have atoms missing, for
example it is supposed to have 1 carbon and 2 oxygen per molecule, but
sometimes it gets only 1 carbon and 1 oxygen. (I uploaded a image, so you
can see this). And what I can do to fix this molecule thing.
my response is essentially the same as above. what you are looking at
are "wrapped" coordinates and if part of a molecule is replaced by its
periodic image, you'll see part of your molecule on one side and the
other part on the other side of the box. this can be avoided by using
visualization tools that can reconstruct unwrapped trajectories and/or
wrap/unwrap by molecule (or fragment).
I am using Lammps version 16Aug13.
which is almost 3 years old. you should consider upgrading, even
though none of your issues from above are related to a specific LAMMPS
version. it is just that there are regularly bugfixes and improvements
added to the package.
axel.
Thank you for your response, Axel.
Ok, so the negative pressure means that the box wants to shrink, because it can’t since the volume is fixed, right?
Also, if I have instantaneous pressure, is there a way to calculate an overall pressure of the box through the simulation? Should I use the pressure at each step?
And I will talk to my supervisor about that. Thanks anyway.