[gmx-users] removing degrees of freedome from different proteins at different timesteps of an md simulation

hi gmx-users, i haven't been able to accomplish the following: i have a system with n atoms, and i want to remove the degrees of freedom for some of the atoms during different moments of the simulation for example, assume the primary sequence of my protein is a-b-c-d-e-f-g, and, for the firs

[gmx-users] simulation confined to a small region

Has anybody had success on running a simulation on only a part of a protein? I have a very large protein, and I'm only concerned with analyzing the motions of two specific close sidechains rather than analyzing the complete system. Do you recommend that I set the simulation box to very very sma

[gmx-users] simulation confied to a small region

I would like to run a simulation on only a part of a protein. I have a very large protein, and I'm only concerned with analyzing the motions of two specific close sidechains rather than analyzing the complete system. Do you recommend that I set the simulation box to very very small dimensions a