[gmx-users] gmx wham

Alex nedomacho at gmail.com
Fri Mar 23 20:46:24 CET 2018

I set things up pretty much according to your tutorial... And yes, there 
are regions of poor sampling from looking at histograms. But those 
poorly sampled regions are also symmetric!!! :)


On 3/23/2018 1:27 PM, Justin Lemkul wrote:
> On 3/23/18 3:22 PM, Alex wrote:
>> My understanding of the value of Z is that it is the distance between 
>> COMs,
>> i.e. that would always be positive -- correct me if i'm wrong. The
> It depends on how you set things up. The displacement is a vector, so 
> you can in principle set things up to have both positive and negative 
> values along the reaction coordinate.
>> configurations in terms of absolute coordinates are as follows: the
>> membrane is at z = 2 nm, the below portion is then 0.5 nm to 2 nm and 
>> the
>> above portion is 2 nm to 3.5 nm. The box is of course 0 to 4 nm in Z. I
>> left all boostrapping options to defaults. The roughness of graphs is on
>> one hand no different from those in the paper first describing 
>> g_wham, but
>> on the other my configurations may be too far apart for the region 
>> near the
>> pore. I suspect it is critical, because this pore pulls things quite 
>> a bit.
>> As far as per-config simulations go, i actually things are sufficient 
>> with
>> 4 ns. I had a set of 10 ns long ones, no difference.
>> Denser spacing between configs?
> Possibly. I'd check the histograms to see if there are any areas of 
> weak sampling that could be skewing things.
> -Justin

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