[gmx-users] gmx wham

Alex nedomacho at gmail.com
Fri Mar 23 20:22:22 CET 2018

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?


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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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