My understanding is, in the Gromacs 2018, we MUST use "-r target.pdb" to
replace the "define = -DPOSRES" option in the .mdp file.
However, how can I do position restraints only for certain atoms, e.g. only the
backbone atoms? I think, if I use "-r target.pdb", both the backbone and side
chain
Hi,
Nothing has changed in the implementation. Atoms which have interactions
specified have always had get position coordinates to target from
somewhere. (Those atoms with no position restraint interactions never
cared.) Historically the position coordinates came from the file you used
for -c if y
Hi Mark,
Thank you for your help! Sorry I was totally confused. I thought I should
delete the "define = -DPOSRES" option and use "-r target.pdb". Now I understand
that.
I should
) still keep the "define = -DPOSRES" in the mdp file
) still keep the "[ position_restraints ]" section in the itp