Reg: merging water reservoir with polymeric membrane

Dear lammps users,

I’m new to molecular dynamics. I want to merge lammps data file of a highly cross-linked polymeric membrane with water reservoir. Polymer box dimensions are 20-60 nm in x,y,z directions. I have created water reservoir using vmd. Water box dimensions are (0,20)x, (20,60)y, (20,60)z. I tried to merge using moltemplate. But my polymer data file has unwrapped co-ordinates. Polymer is highly cross-linked, and 80% of the polymer is outside the box. If i use moltemplate i have to specify new box dimensions in system.lt file, and there we can not specify water box and polymer seperatly. I should not use wrapped co-ordinates of polymer, as that will result in stretched bonds all over the box, and that will be wrong data file.

I’m totally confused with this. Kindly enlighten me with information to solve this problem.

awaiting for your response,

Thanks in advance.

Dear lammps users,

I'm new to molecular dynamics. I want to merge lammps data file of a highly
cross-linked polymeric membrane with water reservoir. Polymer box dimensions
are 20-60 nm in x,y,z directions. I have created water reservoir using vmd.

if you are new to MD, you should not do simulations on complex
multi-component systems. at least not unsupervised.
if i was your adviser, i would make you do simulations of simpler
systems first and then learn the method and the various knobs and
tools first before moving on to more complex simulations.

Water box dimensions are (0,20)x, (20,60)y, (20,60)z. I tried to merge using
moltemplate. But my polymer data file has unwrapped co-ordinates. Polymer
is highly cross-linked, and 80% of the polymer is outside the box. If i use
moltemplate i have to specify new box dimensions in system.lt file, and
there we can not specify water box and polymer seperatly. I should not use
wrapped co-ordinates of polymer, as that will result in stretched bonds all
over the box, and that will be wrong data file.

if you want your polymer film be "mergable", you have to make sure
that while you are preparing and equilibrating it, you have a system,
that is suitable.
one way to do that, is to set up not a fully periodic system, but have
fixed boundaries with soft repulsive walls in the direction, where you
want to expand.
another way could be to create a suitable hole using two regions with
fix oneway (adjacent, but with opposite signs) while also slowly
expanding the box accordingly. this requires, that your molecules can
actually be disentangled within a reasonable amount of time, which may
not be given as you mention high degree of cross-linking.
if you insist on doing this in post-processing, you can try using
pbctools in VMD, which can wrap by molecule, but with a high
cross-link ratio, this may not work out either.

merging multiple data files is easy to do within VMD using the
topotools package. please note, that the solvate plugin may create
data, that is not fully suitable for LAMMPS and may need some
additional post-processing, e.g. removing overlaps.

I'm totally confused with this. Kindly enlighten me with information to
solve this problem.

it is not possible to give a suitably detailed yet simple step-by-step
description for a beginner of the whole process. many details matter,
many things can go wrong, many things can be done in different yet
equivalent ways. learning how to do your work is something that your
adviser should teach you, or somebody that your adviser assigns this
task. do not try to learn this by yourself. you are bound to make a
*lot* of mistakes that are not obvious. you are entering a field with
a large body of work and lots of experience floating around.

axel.