energy minimization

we are trying to energy minimization with bond constraints. please find attached our data file and the input file for the minimization run. we looked into the ‘fix’ commands associated with the minimization run, but couldn’t find any to fox the carbon-hydrogen bonds between the individual atoms.

any help would be appreciated. (9.69 KB)

in.minimization (351 Bytes)

You can use fix restrain:
Or you can use very stiff bonds instead.


This note was recently added to the minimize doc page:

NOTE: The minimizers in LAMMPS do not allow for bonds (or angles, etc)
to be held fixed while atom coordinates are being relaxed, e.g. via
“fix shake”_fix_shake.html or “fix rigid”_fix_rigid.html. See more
info in the Restrictions section below.

The Restrictions section talks about using stiff bond as Michal suggested.