[gmx-users] Packmol starting .pdb and proper equilibration

Ioanna Styliari paxids at nottingham.ac.uk
Thu Oct 30 12:32:29 CET 2014

Thank you both for your prompt replies.

Dr Vitaly Chaban: Is there any way of evaluating how many nodes are needed or is it just by a trial-error approach?

Justin: Although 1fs works, I was aiming for 2fs steps in the MD but it crashes. I was thinking to run the first 2ns with 1fs and then try to continue it with 2fs onwards to see what happens, but it crashed at 700ps of my MD. I am using GROMOS96 53a6.
My equilibration "concern" regards the system: should it be equilibrated as a whole or should I equilibrate one part of it at a time, keeping the others fixed? (which was a suggestion I had but I am unsure how to do it)

Again, thank you


_ _ _ _ _ _ _ _ _ _ _ _ _
Miss Ioanna Danai Styliari
PhD Candidate
Centre for Doctoral Training in
Targeted Therapeutics and Formulation Sciences
School of Pharmacy
University of Nottingham
Email: paxids at nottingham.ac.uk
Telephone: 0044 (0) 74 49890176

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