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Jordi Pina

Change simulation box once in LAMMPS

Dear all,

I have the following problem:

I generate successfully in Polymer Modeler an initial configuration of PE (degree of polymerization 100, 26 chains) in a box of 50Ä.

Once in LAMMPS I want to have the PE on top of a region where I create a lattice of atoms with create_atoms.

The problem is that if I change the simulation box size in the data file I have the following initial result with long bonds between atoms (view down).

This leads to errors like "bond/angle/dihedral extent half of periodic box length".

How could I solve this?

I have found the "solution" of exporting from Polymod the wrapped input file in PDB format and generate the LAMMPS data file by means of VMD and Topotools.

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