Dear All,
I have a quick question regarding how Lammps will handle my procedures below:
(1) I prepared (minimization and equilibration) a membrane-protein system in NAMD, and obtained atoms’ coordinates (unwrapped) and dimensions of the periodic cell from NAMD.
(2) In VMD, I found some atoms (water and some lipids) are actually outside the periodic cell.
(3) I generated Lammps data file using those atoms unwrapped coordinates and their connectives.
My question is: if I also use the dimensions of the periodic cell in Lammps data file and apply periodic boundary conditions, will Lammps assign the atom flag correctly for those atoms outside the periodic cell, and therefore build correct bond, angle, dihedral, improper lists?
Thank you very much for your time and help,
Lili
Dear All,
I have a quick question regarding how Lammps will handle my procedures below:
(1) I prepared (minimization and equilibration) a membrane-protein system in NAMD, and obtained atoms’ coordinates (unwrapped) and dimensions of the periodic cell from NAMD.
(2) In VMD, I found some atoms (water and some lipids) are actually outside the periodic cell.
(3) I generated Lammps data file using those atoms unwrapped coordinates and their connectives.
My question is: if I also use the dimensions of the periodic cell in Lammps data file and apply periodic boundary conditions, will Lammps assign the atom flag correctly for those atoms outside the periodic cell, and therefore build correct bond, angle, dihedral, improper lists?
That is more a question about the tool you use to generate the data file than about lammps.
If the data is prepared correctly, then lammps will behave correctly. Details are in the read_data documentation.
If you still have doubts, then I suggest you create a few small test examples that can be easily verified.
Axel
Many thanks, Axel.
(1) I used ch2lmp tool to generate the Lammps data file.
(2) I just re-visited the read_data doc, and noticed the example for the syntax: read_data data.protein fix mycmap crossterm CMAP, I know Lammps doesn’t support CMAP correction, but it seems there is a fix CMAP in Lammps to do so?
(3) Okay, I will set up some small tests to see how Lammps wraps the atoms (initially outside) to the box and keeps the correct bonding connectivity.
Thank you very much,
Lili
Many thanks, Axel.
(1) I used ch2lmp tool to generate the Lammps data file.
(2) I just re-visited the read_data doc, and noticed the example for the syntax: read_data data.protein fix mycmap crossterm CMAP, I know Lammps doesn’t support CMAP correction, but it seems there is a fix CMAP in Lammps to do so?
This code is not yet released. So you cannot use CMAP.
The read_data doc page explains that for
a periodic box, LAMMPS will read coords outside
the box and remap them into the box.
Steve