Dear doctor:
I’m a student from JiLin university of China. I have a question which has confused me for a long time and I need some suggestion.
For example, there is a system with two kinds of macromolecules , I want to relax two molecules respectivly , and then put them into the samesimulation system.
How can I attain my goal with lammps?
Thanks for your attention and your time .Looking forward your reply
your sincerly
ChenSiyan
Dear doctor:
I'm a student from JiLin university of China. I have a question which has
confused me for a long time and I need some suggestion.
For example, there is a system with two kinds of macromolecules , I want
to relax two molecules respectivly , and then put them into the
samesimulation system.
How can I attain my goal with lammps?
yes, as you can with almost any other MD code.
axel.
Not sure what you mean. But you can do an energy minimization
while holding a portion of the system fixed, via the fix setforce 0.0
command. Then reverse the process.
Steve
What kinds of macromolecules are you trying to simulate?
Do you want to use an all-atom model or a coarse-grained model?
http://en.wikipedia.org/wiki/Force_field_(chemistry)
(I assume you are not interested in electronic degrees of freedom.)
How many copies of each molecule do you need?
Is solvent present? How do you want to represent the solvent?
Andrew