[gmx-users] gmx wham

[Alex]

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
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?

Alex

On Mar 23, 2018 1:11 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:



On 3/23/18 2:23 PM, Alex wrote:
> Which part is unclear? The image is here:
> https://www.dropbox.com/s/eiz1m4b69rr3791/pmf_graphene.jpg?dl=0
>
> "below" and "above" correspond to two sets of ion configs below (-1.5
> nm to 0) and above (0 to 1.5 nm) membrane, respectively. Each curve
> was pinned with -zprof0 1.5. The reason I did not look at the whole
> thing is that I probably got confused by the documentation regarding
> -symm, which suggested relying on PBC when calculating the curve. In
> my case, nothing crosses periodic boundary. The box is ~ 4 nm tall and
> configurations are from z=-1.5nm to z=1.5nm. As you can see, there
> seems to be some sort of a shift going on close to the pore (which is
> at zero)... In any case, the curve above is consistent with my
> expectations, while the one below is not.
>

I would expect the -sym option to be relevant, because the profile, as
you say, should be the same on both sides. However, if you've run the
simulations such that z is always a positive number, this won't work.

How long are the simulations in each window? Have you done bootstrapping
for error estimates? The PMF looks a bit rough so I suspect you may not
have enough data, but indeed the values are strikingly different.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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