[gmx-users] RE: Re: Binding Energy to Binding affinity (Kd) (Justin Lemkul)

Justin Lemkul jalemkul at vt.edu
Thu Oct 4 16:54:28 CEST 2012



On 10/4/12 10:52 AM, jiang wrote:
> Justin Lemkul wrote
>> On 10/2/12 4:39 AM, Du Jiangfeng (BIOCH) wrote:
>>> Hi Justin,
>>>
>>> I used ~20 windows to sample ~2 nm pulling. I notice that the distance
>>> between the complex being increased during the pulling but not gradually.
>>> At the distance of 0-1nm, there are 70 snapshots (the distance sometime
>>> increased sometimes decreased). At the distance of 1-2nm, there are only
>>> 30 snapshots (the distance kept increasing always). At the distance more
>>> than >3nm, the distance increased as 0.3nm of each snapshot, is it normal
>>> and reliable?
>>>
>>
>> I will assume you are using a harmonic potential (umbrella) to do the
>> pulling.
>> In this case, your observations are totally normal.  When two species
>> interact
>> strongly, it is harder to pull them apart, thus the spring extends further
>> to
>> induce a larger force before displacement occurs.  As the restoring forces
>> are
>> overcome, it is easier to move the pulled group through solution, so it
>> makes
>> more steady progress as the molecules are separated.
>
>
> Hi Justin, it is right I am using umbrella pulling. Now here is another
> hurdle in front of me: How to select the snapshots for umbrella samples?
> Since the distance between two groups went higher or lower at the beginning
> of the pulling. For example, during the pulling simulation, the distance
> changes like:
> 0.46 0.42 0.46 0.43	0.44 0.42 0.45 0.44 0.43 0.45 0.44 0.45 0.43 0.44 0.44
> 0.54 0.52 0.63 0.65 0.72 0.8 0.92 1.2 1.5 (nm) .....
> I suppose it doesn't matter which snapshots to be chosen, as long as the
> snapshots can indicate a good spacing, the PMF result always should be same,
> right?
>

You need reasonable spacing and sufficient sampling in each window to allow for 
proper overlap of the umbrella potentials.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
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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