[gmx-users] Perturbation Thermodynamic Integration

[Hannes Loeffler]

On Tue, 16 May 2017 15:13:10 -0400
Dan Gil <dan.gil9973 at gmail.com> wrote:


> If you do this via decoupling ("absolute" transformation) you do that
> > once for molecule A and once for molecule B.  
> 
> 
> I believe you are referring to the BAR method? I am trying to see if
> I get the same results as another group. They used thermodynamic
> integration from A to B, so I decided to spend some more time with
> this. I will try later if I get consistent results for both methods.

No, I am not referring to a specific analysis methods.  I commented on
an alternative pathway.


> transforming the masses may interact badly
> > with bond constraints that are applied to alchemically transformed
> > bonds  
> 
> 
> Thank you for this information! Do you know if there are there
> publications that refer to this issue?

Not that I know of.