On 5/16/12 11:16 AM, Steven Neumann wrote:
On Wed, May 16, 2012 at 3:38 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> 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?
In theory, as long as you've satisfied yourself that this constitutes a
sufficient representation of a non-interacting state, or as close to it as one
can achieve in a system of finite size. I've already said what I think are
reasonable criteria for a preliminary assessment; it's up to you to convince
anyone reading your work that such measurements are sound and appropriate.
-Justin
--
========================================
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
========================================
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