Dear friends
To obtain fix bond length should we use delet_bond command for alkanes instead of shake command?
To obtain stiff spring bonds should we use ‘morse’ bind_style or ‘none’ bond_style ot the other?
would you please help me about this?
Best regards
Nahid
To obtain fix bond length should we use delet_bond command for alkanes instead of shake command?
I don’t know what this question means. I think I already told you that you can’t run
a system in LAMMPS with long alkane chains and fix all the bond lengths.
Steve
dear nahid,
please avoid "spamming" the mailing list with
variants of the same question.
secondly, it looks a lot to me like you first need to learn
some basics about MD simulations. you seem to be
guessing randomly about what to do and several
questions don't make much sense (which probably explains
the lack of responses).
with respect to your questions about "stiffness".
this is a question that you should be able to answer
yourself. if you cannot, then perhaps you need to talk
to somebody (local) that has experience in MD and
stick your nose into a text book on MD simulations
and particularly the chapter about force fields.
with respect to your "lost atoms". that is almost always
an indication of a "bad" starting configuration or "bad"
simulation parameters. the LAMMPS manual has some
suggestions on how to deal with it, since this is one of
the most common error message that people report.
unfortunately, it is also one of the most non-descript
error messages, as there are many causes and you'll
have to monitor your system more carefully to determine
which one. since you don't provide sufficient information,
it is near impossible to provide a qualified answer.
cheers,
axel.
p.s.: if you send mails to mailing lists, please send
plain text only mails. thanks.