I’m trying to carve out part of a field which is already equilibrated and use that as a new simulation setup. From the generated dcd file in equilibration simulation I’ve carved out the desired portion of the field in VMD and used the awesome capability of TopoTools::selections2mol to create pdb and psf files which I use in making the lammps data file using charmm2lammps tool. I have also the data file of the equilibration part.
Now my question is that: How I could include atom velocities of the equilibrium data file in the new data file that includes a portion of the system?
I would really appreciate it if you share your experience on this and help me out.
I'm trying to carve out part of a field which is already equilibrated and
use that as a new simulation setup. From the generated dcd file in
equilibration simulation I've carved out the desired portion of the field in
VMD and used the awesome capability of TopoTools::selections2mol to create
pdb and psf files which I use in making the lammps data file using
charmm2lammps tool. I have also the data file of the equilibration part.
Now my question is that: How I could include atom velocities of the
equilibrium data file in the new data file that includes a portion of the
system?
there is not much of a point in doing that. by cutting out a
subsystem, you have massively changed the potential energy of many
atoms in your system which will quickly transfer (in part) into
kinetic energy. so you need to re-equilibrate your system anyway and
thus simply assigning a new velocity distribution will not be a
problem.