Pack polymer with water without losing bond information.

LAMMPS LAMMPS Mailing List Mirror
1

Hi

I am trying to create a model consisting of a polymer and water. I am modelling the polymer in XenoView and water in Avogadro. Then I want to use Packmol to combine the two. However Packmol requires pdb input files.

PDB file cannot be obtained directly from XenoView. Instead I output a Lammps data file. When I convert polymer data into PDB using VMD or OpenBabel, I am losing my information regarding bonds and angles. I only get one type of bond even though the initial lammps data has 7 types of bonds (which is correct number).

I would be really grateful if you can help me find out a way to solve my problem.

Thank you

2

Hi

I am trying to create a model consisting of a polymer and water. I am modelling the polymer in XenoView and water in Avogadro. Then I want to use Packmol to combine the two. However Packmol requires pdb input files.

PDB file cannot be obtained directly from XenoView. Instead I output a Lammps data file. When I convert polymer data into PDB using VMD or OpenBabel, I am losing my information regarding bonds and angles. I only get one type of bond even though the initial lammps data has 7 types of bonds (which is correct number).

I would be really grateful if you can help me find out a way to solve my problem.

this obviously is a packmol and not a LAMMPS problem. why not use a
different way to combine the topologies?

axel.

3

Hi Axel,

Thank you for your response, but I don't think problem is with packmol. My problem is in converting lammps data file into pdb in VMD. Also, I don't know any other way to combine topologies. Can you suggest some?

Thank you
Manish Gupta

4

Hi Axel,

Thank you for your response, but I don't think problem is with packmol. My problem is in converting lammps data file into pdb in VMD.

no. the fact that packmol cannot preserve topology information, makes
it a packmol problem. there is no conversion to a pdb file that
preserves topology data.

5

Hi Axel,

Thank you for your response, but I don't think problem is with packmol. My problem is in converting lammps data file into pdb in VMD. Also, I don't know any other way to combine topologies. Can you suggest some?

have you searched the web? probably not enough or not used smart
enough keywords for the search. i have at least one posted on my
homepage and there are multiple other suitable tools that are
mentioned in the LAMMPS documentation or elsewhere.

axel.

6

I assume you are building a system of polymers in water. You would typically have ‘N’ copies of water and ‘N1’ polymer chains in solution. You could try doing this via moltemplate. For some typical examples, you can take a look at their homepage. All you need there is an initial coordinate file in xyz for one unit of water and polymer. Using this plus a packmol generated combined xyz, moltemplate can generate the connectivity information in a lammps datafile format.

Look at these examples, http://www.moltemplate.org/. Specifically the way "Many-Body Force-Field Example: mW Solvent + CG Hydrocarbon Mixture" is built.

Regards

Srivastav Ranganathan

Research Scholar

IIT Bombay

Mumbai, India

​