[gmx-users] Free Energy Calculations in Gromacs
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
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
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
> 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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