Hi,
I am working with lammps, and I want to do the MD for a Fuel Cell, using a polymer, water, oxygen, and platinum, and I made a succesfull MD for platinum cluster, but now I want to simulate all the system, but I do not know how to create the psf file to built the input file for lammps, using charmm2lammps.pl, that is for all the system, is about 80.000 atoms.
I apreciate your help, if someone sould help me with that.
thank you so much
Regards
Diego
diego,
Hi,
I am working with lammps, and I want to do the MD for a Fuel Cell, using a
polymer, water, oxygen, and platinum, and I made a succesfull MD for
platinum cluster, but now I want to simulate all the system, but I do not
know how to create the psf file to built the input file for lammps, using
charmm2lammps.pl, that is for all the system, is about 80.000 atoms.
to build a .psf file you can use either the psfgen tool that comes with
NAMD or VMD or use the CHARMm software.
rather than creating the psf file, you could also write a small script/program
that creates the lammps data file directly. there is a script to do this that is
part of the topotools plugin in VMD.
however, to be able to do _either_ you first need to have the force field
parameters to describe _all_ interactions in your system, and i would be
surprised, if there are CHARMM parameters for all atom types that you need.
you will most likely have to use a hybrid potential approach.
in any case, before thinking about file formats, check out what
potential parameters you would need and where you can find them.
cheers,
axel.