Thank you very much for your help.
I think that I finally got this straight.
Cheers,
Rui
On 27 September 2016 at 11:26, Hannes Loeffler
wrote:
> On Tue, 27 Sep 2016 11:08:45 +0100
> Rui Neves wrote:
>
> > However, what I would like to know is:
> > At the beggining of the topology I call for
On Tue, 27 Sep 2016 11:08:45 +0100
Rui Neves wrote:
> However, what I would like to know is:
> At the beggining of the topology I call for all the bonded terms
> ('#include ffbonded.itp), and then in the [ atoms ] section, I
> specify the massB, typeB and chargeB for the B-state. Do I have to
>
Hi Billy,
Thank you so much for the papers you suggested. I hadn't come across them.
However, what I would like to know is:
At the beggining of the topology I call for all the bonded terms
('#include ffbonded.itp), and then in the [ atoms ] section, I specify the
massB, typeB and chargeB for the
Hi there,
Because the bond and angle parameters are harmonic terms in many
forcefields, my understanding is that they should cancel out during a
closed thermodynamic cycle. So you will not need state B parameters for
those terms.
However, you will need to state state B terms for proper and impro
Hi Gromacs users,
I am trying to determine a relative binding free-energy of two hypothetical
ligands (A -> B).
To do this, I must indicate a typeB for the atomtypes in B.
Once this is done, do I have to explicitly include the bonded parameters
for the B state, if I started by loading all the par
