Potential Recommendation or Fix One?

Dear LAMMPS Users,

I am trying to build a model of a cell membrane with water inside and outside of it, similar to the model made in this paper .

This Video shows the most recent simulation I have made a rendering of. The membrane holds together but most of the inside water ( from here this will be called “plasma” ) escapes very quickly out of the membrane.

( Also included in my .in file )

I think this is due to a few factors:

I found that the bonding in the membrane needs to be adjusted, currently the bonds extend to up to 2 “neighbor particles” on the membrane away, yet I have the same bond lengths for if this was 1 or 2 initial units away

The Potential I am using for all particle types is the lj/cut potential, I am trying to use the method and custom potential used in the paper linked earlier, however I think since the paper is a few years old the included files are not compatible with the current version of LAMMPS, as I cannot run them.

Lastly in the shown simulation the density of Plasma within the membrane was much higher than the density of the water outside, this probably led to a lot of the behavior as well and I am currently developing/running/rendering a simulation with the densities of the Plasma and water equal.

So ultimately my questions are:

Is there a Potential that is included with LAMMPS that is better for a Cell Membrane?

or

Can I get the fluidmembrane Potential from the Linked Paper working if I did something different? ( Currently I have just tried adding the C and header files to my src and then rebuilding LAMMPS , but no dice)

Thanks for reading,

Jack

Preview attachment in.Plasma_H2O_Test_V9.4

in.Plasma_H2O_Test_V9.4
1 KB

The .in file I forgot to attach

[

](https://mail.google.com/mail/u/0?ui=2&ik=483273cbdc&attid=0.1&permmsgid=msg-a:r4663725486663216251&th=173d9037b7342da0&view=att&disp=safe&realattid=f_kdoogudi0)

Dear LAMMPS Users,

I am trying to build a model of a cell membrane with water inside and outside of it, similar to the model made in this paper .

This Video shows the most recent simulation I have made a rendering of. The membrane holds together but most of the inside water ( from here this will be called “plasma” ) escapes very quickly out of the membrane.

( Also included in my .in file )

I think this is due to a few factors:

I found that the bonding in the membrane needs to be adjusted, currently the bonds extend to up to 2 “neighbor particles” on the membrane away, yet I have the same bond lengths for if this was 1 or 2 initial units away

The Potential I am using for all particle types is the lj/cut potential, I am trying to use the method and custom potential used in the paper linked earlier, however I think since the paper is a few years old the included files are not compatible with the current version of LAMMPS, as I cannot run them.

you can download older versions of LAMMPS from http://lammps.sandia.gov/tars or https://github.com/lammps/lammps/releases

or you can check out the files for the custom pair/bond styles and port them to the current version by comparing them to a similar existing style.

you can also try to contact the authors of the paper to ask whether they have updated versions.

Lastly in the shown simulation the density of Plasma within the membrane was much higher than the density of the water outside, this probably led to a lot of the behavior as well and I am currently developing/running/rendering a simulation with the densities of the Plasma and water equal.

So ultimately my questions are:

Is there a Potential that is included with LAMMPS that is better for a Cell Membrane?

that is too generic a question. there are many different models and the model determines which potential to use. so your best path to find an alternative would be to search the published literature.

or

Can I get the fluidmembrane Potential from the Linked Paper working if I did something different? ( Currently I have just tried adding the C and header files to my src and then rebuilding LAMMPS , but no dice)

to learn how to add a custom potential to LAMMPS, I recommend you carefully study the section of the LAMMPS manual about modifying and extending LAMMPS.
it should give you sufficient background in what is needed to integrate modified or custom sources into the distribution and how to compile them. it expects a sufficient familiarity with C++ programming and compiling/linking code from sources. there is plenty of material for that available online and in books on C++ programming.

axel.