Equilibration using OpenMM
Posted: Tue Jun 11, 2019 2:56 pm
Hi all
I've been using OpenMM for a while on solvated and equilibrated structures obtained using other means. I was wondering if anyone uses OpenMM to equilibrate a large protein from the initial crystal structure. This would involve
* Solvation using a pre-equilibrated water box or something similar, and adding ions to counter the charge
* Optimizing water positions (MC maybe)
* Relaxing the protein structure to accommodate (restraints/minimization/decaying restraints)
Different groups have different philosophies on equilibration and getting a protein ready for MD, but I'm wondering what the latest and greatest is, and whether this can even be done using OpenMM only.
I've been using OpenMM for a while on solvated and equilibrated structures obtained using other means. I was wondering if anyone uses OpenMM to equilibrate a large protein from the initial crystal structure. This would involve
* Solvation using a pre-equilibrated water box or something similar, and adding ions to counter the charge
* Optimizing water positions (MC maybe)
* Relaxing the protein structure to accommodate (restraints/minimization/decaying restraints)
Different groups have different philosophies on equilibration and getting a protein ready for MD, but I'm wondering what the latest and greatest is, and whether this can even be done using OpenMM only.