Hi all!

Could anyone explain and clarify whether it is possible to run Random Accelerated Molecular Dynamics Simulation in gromacs environment?

Here is a list of associated papers, which describe similar studies conducted with CHARMM, NAMD and, in addition, claim that there is nothing complicatec in runing of the protocol within GROMACS:

* Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor ( 10.1017/S0033583515000153 )

* Molecular Dynamics Simulation of Ligand Dissociation from Liver Fatty Acid Binding Protein (10.1371/journal.pone.0006081)

* Accelerating Dissociative Events in Molecular Dynamics Simulations by Selective Potential Scaling (10.1101/547307)

all of them reffered to the oldest paper:

How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms. (10.1006/jmbi.2000.4154)

I've searched for attached script in 10.1371/journal.pone.0006081 and also have wrote an email to the authors, but they ignored my query.

It could be more convenient to try another package, which contains the exact code. But I don't want to transfer from GROMACS, because the work is already done (3 mutations + wt protein, dimerization interface study, binding site geometry fluctuations, cavity analysis and so on), I just want to simulate the effect of mutation on the binding site closure in presence of the ligand...

Thank You all !!