[gmx-users] putting step wise constraints in energy minimization

[Justin Lemkul]

On 2/14/20 2:21 PM, Sadaf Rani wrote:
> Dear Gromacs users
> I want to run energy minimization in steps
> first to remove clashes with ions, second keeping position of heavy atoms
> fixed and thirdly removing all constraints. How can I set this in mdp file
> for ions and protein atoms?

What you're referring to are restraints, not constraints. "define = 
-DPOSRES" restrains heavy atoms, so use that and then turn it off in the 
next round.

-Justin

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Justin A. Lemkul, Ph.D.
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