[gmx-users] Umbrella Sampling

[Steven Neumann]

Thank you a lot!


On Wed, Jul 31, 2013 at 12:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/31/13 6:52 AM, Steven Neumann wrote:
>
>> 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?
>>
>>
> I can offer you nothing more than a hand-waving explanation of what I
> think might happen here, so take that for what it's worth.  Since you
> explicitly asked for my thoughts, such as they are...
>
> The dissociation of the ions may be nothing more than an artifact of the
> pulling conditions.  Have you tried different force constants and pull
> rates to see if this behavior is affected?
>
>
>
>> 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.
>>>
>>>
> Even though you're not explicitly pulling the ions, they are being forced
> to move due to the biasing potential that you are applying.
>
> I would think that sufficient sampling in each window (i.e. enough time
> that you might see dissociation of the ions) would provide you with enough
> information, but that's hard to predict.  My assumption would be that the
> ions will absolutely impact the free energy of binding, but from what you
> said above, maybe that's right.  Maybe it's not.  Only way to find out
> would be to either exclude the ions or otherwise restrain their initial
> positions so that you get a "clean" reaction coordinate involving only the
> ligand.  Then you can decompose the different contributions to the free
> energy of binding.
>
> -Justin
>
>
>>> 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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>>>
>>>
> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
> ==============================**====================
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