normal Reverse Transformation mdp file

  • anna_duncan
  • anna_duncan's Avatar Topic Author
  • Offline
  • Fresh Boarder
8 years 4 months ago #960 by anna_duncan
Reverse Transformation mdp file was created by anna_duncan
I'm carrying out reverse transformation on a single protein molecule for the first time. I'm a bit unclear on the way to release the coarse-grain restraints (the last stage); is this supposed to be run as a separate simulation, after the simulated annealing step, or can it be run from the same mdp file as the simulated annealing stage?

More specifically, I have an example mdp file, fg.mdp, from the reverse transformation tutorial. In this file dt = 2 fs, nsteps = 40000, rel_steps = 0, annealing = single, annealing time = 0 60 etc.. Should I run a first simulation with these settings, and then change rel_steps to 5000 (as suggested in the paper for this topic, Rzepiela et al., 2010 ), nsteps to 5000, with annealing = no for a second simulation?

Please Log in or Create an account to join the conversation.

8 years 2 months ago #1052 by jantunes
Replied by jantunes on topic Reverse Transformation mdp file
Hey anna,

I think you just have to do one simulated annealing, with rel_steps = 5000. The last 5000 steps (from the 40000) will have the constrains gradually removed.



Please Log in or Create an account to join the conversation.

Time to create page: 0.098 seconds