[gmx-users] PMF profile from Umbrella - Plateau

[Steven Neumann]

On Wed, May 16, 2012 at 3:38 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/16/12 10:25 AM, Steven Neumann wrote:
>
>> Dear Justin,
>>
>> I pulled my ligad away of 6nm from the protein and obtained beautiful and
>> smooth
>> curve of PMF using 28 windows. Starting from zero kcal/mol corresponding
>> to app
>> 0.3 nm then minima and curve increase till my plateau which starts from
>> app 1 nm
>> - then I have nearly straight line till 6.3 nm.
>> My question: Can I decrease pulling distance to save time for the future
>> simualtions with this system in terms of number of water molecules? Shall
>> I just
>> pull it away of 2-3 nm and I will obtain the same deltaG?
>>
>>
> Ideally, one would separate the molecules such that they are no longer
> interacting.  Obviously with methods like PME this is impossible, so what
> you're after is sufficient separation such that there is negligible
> interaction between the protein and ligand.  The required distance depends
> on the nature and size of the ligand, the types of interactions it
> experiences, and the cutoffs used. Keep in mind that even if a molecule is
> beyond the longest nonbonded cutoff, there are still effects like water
> ordering that can persist up to about 1.0 nm, so I would certainly make
> sure that all the atoms of the ligand and protein are separated by a
> minimum of twice the longest cutoff or so to account for this effect.  Note
> that this would imply the use of g_mindist, not g_dist, as the distance I'm
> talking about is not the same as the COM distance.
>
> That's just my own rule of thumb for an initial check; you'll have to
> analyze your own system to decide what's happening and what you should do.
>
> -Justin
>

Thanks Justin! I totally agree. But now having my ligand pulled 6 nm away
and obtained deltaG= -4.5 kcal/mol. In theory when I use all windows till
3.5 nm (not till 6.3 nm) and I will obtain the same value it means that I
can decrease the pulling distance in future simulations. Am I right?


Steven

>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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