[gmx-users] Umbrella Sampling

[Steven Neumann]

But even though on the other hand that could be more realistic free energy
which could be compare to experiment which also involves ions. Would Justin
please comment on this?


On Wed, Jul 31, 2013 at 11:46 AM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> 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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>
>