Problem with density profile

Dear All users

I have a confined system, decane molecules(united atoms) between gold
walls and I did npt ensemble at 300 k and 1 bar,

I have a problem with mass density profile and ave/spatial

I used this command for computing mas density profile in y deirection

group decane type 2 3 # 2: ch3 group and 3:ch3 group

..

fix 12 decane ave/spatial 100 100 10000 y 0 0.1 density/mass ave one
units box file density
...
run_style verlet
run 1000000

My average density is .783 while bulk density is .726 gr/cm^3

I calculated my total number of molecules by that value(.783) for
density, The total number of molecules are 243 but in my simulation
box are 340 chain,

Can any body help me?

density.jpg

Can any body help me?

Not unless you have some evidence
that LAMMPS is doing something wrong.

If you are simply getting a different answer
than you expect, that is really your job
to figure out why.

Steve

Dear Steve

Thank you for your reply,

Not unless you have some evidence
that LAMMPS is doing something wrong

No, I think my sampling can be wrong or That command can not calculate
exactly the profile that is related to molecules density because my
group command is related to 2 or 3 type not individual molecule,

Dear Steve

Thank you for your reply,

Not unless you have some evidence
that LAMMPS is doing something wrong

No, I think my sampling can be wrong or That command can not calculate
exactly the profile that is related to molecules density because my
group command is related to 2 or 3 type not individual molecule,

you're not making much sense here.

it is difficult to give any advice, since there is not much
information to go with your question. for starters your system looks
like you have two layers and it is not clear how you compute the
density that you claim you have.

as i advised you earlier. you can't just go and do some simulation
using a tool that you don't understand. so you have to teach it to
yourself in steps.

before doing anything complex like a confined system, start by doing
a simulation of a bulk system at constant volume (nvt). for this you
*do* know the density and your analysis should show the same density
in your averaged density profile. if it doesn't, something more
fundamental is wrong.

as a next step, you should do a variable cell (npt) md of a bulk
system and check if the density you expect is consistent with your
force field. if it isn't, you have to investigate whether this is
meaningful, consistent with the description of the force field, or
whether you may have an error in your input deck.

only after all those tests have worked and you are familiar with
computing density profiles, you should move to your confined system.
at that point you have to check, why you get such a strong adsorption
(wrong parameters?). if you set up the calculation correctly, you
should get a bulk region with a density comparable to the variable
cell run. if not, you have to check again and debug.

nobody can do this for you and *this* is the nuts and bolts of doing
meaningful MD studies, *not* being able to run a simulation and make
some atoms wiggle.

axel.

Dear Axel

Thank you very much for your complete reply,

I will do those steps!

Ali,

Even very clever people know that in order to make substantial progress in your studies you need to be close

to where things are happening. Technology helps you to have access to much knowledge from a far but it doesn’t

substitute a good mentor/adviser. People always move around looking to work/interact with those who know best. Sometimes I wonder what kind of support people like you have in their local universities when you are posting questions of the kind you drop in this list. If you are just somebody working on a term project then disregard my words. However, if you are serious about getting into this business for real, you should look for a way to join a group where you have peers that can help you move forward. If you chose not to take action, at some point the gap in knowledge will be so large that there will be nothing you can do to catch up.

Carlos

PS: I know this is not a LAMMPS related answer, yet, consider it a reminder that life is not fair and nobody is

going to take you where you need to get.