[gmx-users] Free Energy Calculations in Gromacs

Michael Shirts mrshirts at gmail.com
Sat Apr 20 23:52:57 CEST 2013

You have to change atom types.  For example:

[ atomtypes ]
;name  bond_type    mass    charge   ptype          sigma      epsilon
h1            h1         0.0000  0.0000      A      2.47135e-01  6.56888e-02
h1_pert     h1         0.0000  0.0000      A      2.47135e-01  3.56888e-02
; perturbed

The mass and charge can be zero, because they will be defined in the [
atoms ] part

[ atoms ]
;   nr    type  resnr residue  atom  cgnr  charge    mass    typeB
 chargeB  MassB
    1     h1      1     BLAH    H1a     1     -0.089    1.008    h1_pert
 -0.030  1.008;  perturbed

On Sat, Apr 20, 2013 at 4:04 PM, HANNIBAL LECTER <hanniballecter13 at gmail.com
> wrote:

> 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 the similar terms of State A.
> It's not quite clear to me (going through the archives of the gmx-users
> mailing list how to perform these calculations. One way to do this, is to
> use a single topology file in which the charges and the other terms are
> specified for both states A and B. However, it is not clear as to how
> should I scale the epsilons in the topology file. (My atoms are not mutated
> in state B. They are the same atoms with scaled epsilons.)
> Secondly, since I have the topology files for states A and B, is there a
> way I could perform the simulations (any particular way in grompp) where
> both the topology files can be preprocessed designating the end states and
> using the mdp options, the simulations corresponding to the intermediate
> lambda values performed??
> --
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