[gmx-users] Umbrella Sampling

[Steven Neumann]

They do not dissociate...Are you sure? My mdp specifies only ligand as a
pull_group1. I think it would change having ions in this group included.


On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs <lloyd.riggs at gmx.ch> wrote:

>
> >will get the PMF profile for my
> >ligand binding or ligand and two ions binding?
>
> It would be the ligand and two ions unless the ions also at some point
> discossiate from the ligand once in solvent. Could add positional restraint
> for them, but dont know how that effects the calculation?
>  *Gesendet:* Mittwoch, 31. Juli 2013 um 09:29 Uhr
> *Von:* "Steven Neumann" <s.neumann08 at gmail.com>
> *An:* "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> *Betreff:* [gmx-users] Umbrella Sampling
> Dear Gmx Users,
>
> I run SMD to extract the windows for US calculations. The system involves
> negatively charged ligand and protein. I generated the protein-ligand
> complex within self assembly MD simulations.
>
> I pulled my molecule away and two ions were also detached from the protein
> surface being attached to my ligand.
>
> My question: if I run my US caluclation and combine windows by WHAM (I
> specified in my umbrella.mdp my ligand as a pull_group1 and same protein
> residues I pulled it from as pull_group0) will get the PMF profile for my
> ligand binding or ligand and two ions binding?
>
> Steven
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