Hi LAMMPS users,
I am new to LAMMPS and I am seeking some help to create my super cell, I am confused about when can I use codes like packmol to create me cell by replication and when can I use the “lattice command”.
I am creating a zircon cell with body center tetragonal crystal structure. I used packmol to replicate the coordinates but I found a note in one of the questions in the mailing list stating that packmol is a powerful tool but creates only coordinates and we need to use another code to create the molecular topology.
I know that it is a primary question but i am in a very bad need to direct me some clues or just direct me how to search about this.
Thanks in advance.
Meral
Hi LAMMPS users,
I am new to LAMMPS and I am seeking some help to create my super cell, I
am confused about when can I use codes like packmol to create me cell by
replication and when can I use the "lattice command".
I am creating a zircon cell with body center tetragonal crystal structure.
I used packmol to replicate the coordinates but I found a note in one of
the questions in the mailing list stating that packmol is a powerful tool
but creates only coordinates and we need to use another code to create the
molecular topology.
whether you need a topology depends on your choice of force field.
typically, it is only required for molecular force fields.
you can replicate a system also from within LAMMPS (replicate command).
I know that it is a primary question but i am in a very bad need to direct
me some clues or just direct me how to search about this.
your question is quite vague and your apparent need of general tutoring
and advising is usually best done by talking to a local person with
experience in MD simulation. start with your adviser/supervisor. a mailing
list like this one is focusing on specific issues with a particular
software is ill suited to provide that kind of fundamental training and
advice.
axel.
Thank you Axel for your reply, I really appreciate it. Is there a chance you suggest me a guide book to learn the basic steps as my supervisor is also starting to learn and know about the MD field.
Thank you,
Regards
Meral
Hi LAMMPS users,
I am new to LAMMPS and I am seeking some help to create my super cell, I am confused about when can I use codes like packmol to create me cell by replication and when can I use the “lattice command”.
I am creating a zircon cell with body center tetragonal crystal structure. I used packmol to replicate the coordinates but I found a note in one of the questions in the mailing list stating that packmol is a powerful tool but creates only coordinates and we need to use another code to create the molecular topology.
whether you need a topology depends on your choice of force field. typically, it is only required for molecular force fields.
you can replicate a system also from within LAMMPS (replicate command).
I know that it is a primary question but i am in a very bad need to direct me some clues or just direct me how to search about this.
your question is quite vague and your apparent need of general tutoring and advising is usually best done by talking to a local person with experience in MD simulation. start with your adviser/supervisor. a mailing list like this one is focusing on specific issues with a particular software is ill suited to provide that kind of fundamental training and advice.
axel.
the Allen & Tildesley book is a good one.
Steve
Thank you Axel for your reply, I really appreciate it. Is there a chance
you suggest me a guide book to learn the basic steps as my supervisor is
also starting to learn and know about the MD field.
there is a bunch of them. some more technical than others. some more
modern than others. if would suggest something that discusses not just the
theory, but has some examples of how simulation software and analysis
software is implemented.
the book "understanding molecular simulations" by frenkel and smit is
frequently recommended.
axel.