[gmx-users] Free energy calculation problem with too high dG

[Hannes Loeffler]

On Tue, 4 Oct 2016 13:08:51 +0300
Vlad <vlad_balaev at mail.ru> wrote:

> It appears in the step where ligand starts to recouple (I start
> from the decoupled ligand and consequently turn on vdw and then
> charges). And the dG between the zero and the first init_lambda
> appears about 1800 kJ/mol

Is there any particular reason why you cannot run a decoupling
simulation?  Creating a molecule out of "nothing" will need to push
existing atoms aside and I can see why that could be a problem.  
Have you checked the trajectory to see what is happening?


Cheers,
Hannes.