Re: [gmx-users] What is the equivalent way to do postion restraints only for backbone atoms in Gromacs 2018?

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

Re: [gmx-users] What is the equivalent way to do postion restraints only for backbone atoms in Gromacs 2018?

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

[gmx-users] What is the equivalent way to do postion restraints only for backbone atoms in Gromacs 2018?

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