I have difficulty with vacuum gap

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1

Dear Users,

I have a system with propane molecules(opls-aa force filed) and a surface. In my system

and in x direction at first I have a surface and then above this surface I have propane

molecules. I have a problem, my molecules can sense below my surface(I’ve attach two my

snapshots of initial configuration and final configuration that include gap below my surface but I can not this gap in vmd. I used these two lines for visualizing in vmd :

pbc wrap -compound res -all
pbc box
)

while it should not occur besides I should use pbc in all directions. All of my molecules should

have interaction with above of my surface.

According to my prior email and reply I add extra space by increasing

the length of my box in x direction for having a vacuum slab below my surface. But After running

I got the same results which I have pbc in all directions and without gap below my surface.

Does LAMMPS ignore this vacant room below my surface?

My prior post :

I want to add a gap between my surface and molecular environment. Are ther any options in vmd

for performing this? Or Can I add a gap wherever in my simulation box? I want to omit the

interactions between them, my surface(crystal) and molecules.

In my view one probable approach can be this but I am not sure about it,

My system should be pbc in all directions. I want to add this gap below the end of my

structure therefore when I write the system.data after that I will increase the box size in direction

x while there are not any atoms from the bottom of my system to my structure.

Is it possible? or Will Lammps perform it what I want to reach?

final.jpg

initial.jpg

initial before wrapping.jpg

2

You appear to have a problem with the repulsive part of your potential between propane molecules and the surface. Your propane seem to be happy to overlap with surface atoms. Check by testing with the surface and only one propane molecule. The LJ part of the OPLS FF should take care of repelling the propane form the surface. The question is, what kind of parameters you employed for the surface - propane interactions. OPLS was originally developed for liquid simulations (hence its name). I would suspect use of its parametrization on surfaces unless further evidence is provided to support such a usage.

Carlos

3

Dear Carlos,

Thank you very much for your reply.

Apparently my molecules overlap with my surface but in fact they do not overlap. Parameters are LJ for interaction between them.

You mean my parameters lead to happen this. What do you think about adsorption on my surface? You believe that my molecules have

strong repulsion force with my surface? My density profile shows that they have been absorb on my surface.

4

Besides I want to know can I have vacuum gap in my system so that it does not allow my molecules to interact with one side of my surface.

5

Dear Users,

I have a system with propane molecules(opls-aa force filed) and a surface.
In my system

and in x direction at first I have a surface and then above this surface I
have propane

molecules. I have a problem, my molecules can sense below my surface(I've
attach two my

snapshots of initial configuration and final configuration that include
gap below my surface but I can not this gap in vmd. I used these two lines
for visualizing in vmd :

    pbc wrap -compound res -all
    pbc box
)

while it should not occur besides I should use pbc in all directions. All
of my molecules should

have interaction with above of my surface.

According to my prior email and reply I add extra space by increasing

the length of my box in x direction for having a vacuum slab below my
surface. But After running

I got the same results which I have pbc in all directions and without gap
below my surface.

Does LAMMPS ignore this vacant room below my surface?

please keep in mind. LAMMPS doesn't care what you want and never will. it
looks at what interactions you define, computes the interactions and moves
the atoms.

everything else is up to you.

axel.

6

Dear Axel,

Thank you for your reply.

I wanted to use slab bc but it is not possible because of my Ewald kspace option. Are there any options to build such this system z and y are pbc and

x is not pbc?

7

Dear Axel,

I found this post which includes your advice about slab creation. In your opinion it can be useful for my case?

Because I want to have this system I created the gap in my system based on this idea. But I do not know

why my method did not work.

8

Dear Axel,

I found this post which includes your advice about slab creation. In your opinion it can be useful for my case?

Because I want to have this system I created the gap in my system based on this idea. But I do not know

why my method did not work.

http://lammps.sandia.gov/threads/msg32588.html

9

I’m a bit confused about your what your exact problem is, but if your first pic is not a top view it looks to me as if the propane was getting embedded into the surface. You seem to have a problem with your interactions thus my old advice still applies. Simplify your problem, one molecule vs surface, make sure your parameters are in the right unit system, etc, etc. If your parameters are correct as you appear to claim then hopefully someone else will reply with other ideas for you.
Carlos

10

Dear Axel,

I found this post which includes your advice about slab creation. In your
opinion it can be useful for my case?

you must not ask for *my* opinion, you have form *your own* opinion. if you
don't understand the elementary steps of what you are doing, how can you
make choices in a complex input.

Because I want to have this system I created the gap in my system based on
this idea. But I do not know

why my method did not work.

it doesn't work, because you expect a
ready-to-use-no-question-about-it-works-always solution to drop from the
sky right into your lap. i already told you several times, that this is not
how you can operate and i've said many times that a mailing list is no
replacement for getting advice from a knowledgeable adviser or senior
colleague. more importantly, by just iterating the same problem without
doing any proper thinking and deduction by yourself, you effectively try to
outsource what is *your* work to the mailing list. that is not going to
work. you may find a sucker on and off but in the long run all you'll
achieve with that is that you exhaust people's willingness to help you. i
am right at this point, for example. a couple more of these unreflected
questions, your e-mail address will join my "kill file" of e-mails that get
directly sent to the trash folder without me ever looking at it.

axel.