[gmx-users] Apply position restraints to part of RNA molecule

[闫舒婷]

Dear gmx users,

I am working on simulating a RNA aptamer with GROMACS. I want to apply
position restraints to only part of the molecule during equilibration. I
created an .itp file including those atoms which I plan to make restrained.
I defined position restraints in .mdp file, and in the .top file, I also
included that ,itp file. I am not sure whether what I did is correct, for I
didn't observe a difference. I also tried to use -r flag with an ,gro file
including those atoms, when I used grompp. But there appeared fatal error
notification saying that the the number of atoms didn't match. I was also
thinking about doing something with the .top file for example writing three
molecule type instead of one, but I thought that might be crazy. I am
confused. Could anyone give me a hint? Thank you for your time.

Sincerely,
Shuting Yan