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Setup, I/O, and Basic questions
Jump to new posts Re: How to keep residues across a specific range? by jtyang @ Yesterday at 09:23 PM

thanks for your reply, especially about the "imall" option, this is what I use after recheck the doc file, "imall" added twice because I don't know on which line it will work, I hope there are no new problems, it looks like OK for me: ... imag byre s
Molecular Dynamics
Jump to new posts Re: Implicit solvent simulation by Ashd @ 06/13/19 09:40 PM

Dear All, I am trying to run an equilibration for a large protein (1 MDa) using the GBSA method. Could anyone suggest me a tutorial to follow in order to set up the system? Thank you!
Energy terms, Constraints, Restraints, and Solvation
Instead of trying to fix the molecule in place during step6_equilibration, could I let those steps run unconstrained, do one step in production and then edit the coordinates/velocities from my gas phase dynamics into the restart file? I realize that