Re: [gmx-users] Free Energy Calculations in Gromacs

Thank you Professor Shirts. So now my protein itp file looks like this: [ atoms ] ; nrtype resnr residue atom cgnr chargemasstypeB chargeB MassB 1 CT1ACECH3 1 -0.190264 12.01 CT_per -0.12033412.01 [ bonds ] ;ai aj func th0 kb th0

Re: [gmx-users] Free Energy Calculations in Gromacs

You have to change atom types. For example: [ atomtypes ] ;name bond_typemasscharge ptype sigma epsilon h1h1 0. 0. A 2.47135e-01 6.56888e-02 h1_pert h1 0. 0. A 2.47135e-01 3.56888e-02 ; perturbed The

[gmx-users] Free Energy Calculations in Gromacs

Hi, I am trying to perform expanded ensemble simulations between 2 states A (lambda=0) and B (lambda =1) with 6 intermediate lambda values. In state B the Hamiltonian is rescaled, such that the epsilons of the vdW interactions, the charges, the bond, angle and dihedral constants are a multiple of