Problem with use charmm2lammps.pl

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1

Hi dear Lammps users:

I use charmm2lammps.pl for creating my lammps data and input file. I have a problem with it. I use option -water to add TIP3P water to my box and and I use options -lz=65 and -ly=33 and -lx=33 for define my box dimensions. Also I have one protein in my box and one of special atom of protein is located in zero coordinate (0,0,0). Now I would like to spread waters around zero coordinate not around center of mass of my protein. How I can do this? It is very important to me.

Thanks in advance

Xuequing Lu

2

Sounds to me like it might be easiest to create a box that is bigger than you need, with too many waters, then read it into LAMMPS and delete the water you don’t need.

See:

http://lammps.sandia.gov/doc/delete_atoms.html

particularly the region option. See:

http://lammps.sandia.gov/doc/region.html

Paul