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

[Vlad]

No reason. I just thought it would give the same result. Now I launched a simulation with decoupling (without md and with few number of lambda values - only for testing). Hope it will end in an hour

In the trajectory the ligand diffuse to the end of the cell like a ghost through the water molecules.
And could the reason lie in the fact that in the initial structure during all preparations the ligand is "fully existing" and in the first step of simulation suddenly is turned off?

Sincerely yours,
Vlad

>Вторник,  4 октября 2016, 13:50 +03:00 от Hannes Loeffler <Hannes.Loeffler at stfc.ac.uk>:
>
>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.