Hello everyone, I performed an MD simulation for 50 ns by imposing a restraint (by adding the necessary information at the very ending part of my topology file:
; distance restraints for 2atoms-in-prot-lig
[ intermolecular_interactions ]
[ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
5059 5152 1 0 1 0.0 0.3 0.4 1.0
)
Now, I want to extend my MD but I want to remove the restraint). Naturally, I need to delete those lines at the end of the topol.top file and by using “gmx convert-tpr”, create the new tpr file. But, in this way, my new tpr file won’t have the information of the new topol.top file. Do you know what should I do?
A common way is to put your restraints in a separate .itp file, and include it (from your .top file) if there is a corresponding define statement in the .mdp file. I’m sure you can find examples of it.
It’s usually a good idea to avoid editing your topology more than necessary. But why not generate the new .tpr with gmx grompp?
You are right. I try to generate a new .tpr with gmx grompp.
Thank you