Hello dear lammps users
In my simulation box, I have two separated regions in which I have the same solution with different numbers of atoms. I have two problems to make data and input file for this setup:
-
After I use automatic psf builder tool in VMD for a pdb file which contains all of the atoms in both regions so that I would be able to generate a single data and input file for both solutions by using charmm2lammps, the total number of atoms decreases. Why does this happen and how can I fix it?
-
By using automatic psf builder tool in VMD for each region, separately, I made two different psf file and with charmm2lammps I made two different data and input file. How can I merge two different data file with preserving the number of atoms, bonds, angles, dihedrals, and types?
Thanks,
Toon
Hello dear lammps users
In my simulation box, I have two separated regions in which I have the same solution with different numbers of atoms. I have two problems to make data and input file for this setup:
1. After I use automatic psf builder tool in VMD for a pdb file which contains all of the atoms in both regions so that I would be able to generate a single data and input file for both solutions by using charmm2lammps, the total number of atoms decreases. Why does this happen and how can I fix it?
No idea. Hopefully someone else replies.
2. By using automatic psf builder tool in VMD for each region, separately, I made two different psf file and with charmm2lammps I made two different data and input file. How can I merge two different data file with preserving the number of atoms, bonds, angles, dihedrals, and types?
This topic came up a few times. Here's a link to a discussion that
might be helpful
https://lammps.sandia.gov/threads/msg78460.html
When I posted that message I mistakenly omitted topotools. Topotools
is also very useful for merging two data files together:
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---various-tips-tricks
Incidentally, if you haven't seen it, there's a list of other tools
for creating DATA files and input scripts at this web page:
https://lammps.sandia.gov/prepost.html
But if my memory is correct, and if you are using the CHARMM force
field, then either charmm2lammps.pl (the script you are using) or EMC
are probably your best options (currently at least).