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

jiang j.du at maastrichtuniversity.nl
Thu Oct 4 16:52:05 CEST 2012

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,

Thanks, jiang.

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