[gmx-users] RE: Re: RE: Re: Wierd results from Umbrella sampling (Justin A. Lemkul)

Du Jiangfeng (BIOCH) j.du at maastrichtuniversity.nl
Tue May 22 15:39:42 CEST 2012

Hi Justin,

As for the maximum of 0.4 nm fluctuation of my pulled protein, I used g_dist to calculate the distance between my pulled protein and stable part in a window, where the distance is treated as the fluctuation of the protein along z-axis.

Well, from pullx.xvg, the position moved a lot (3nm for instance.)

As for the windows simulation, I didn't apply constraint but only the internal constraint in the itp file. I still don't understand why it have to do constraint? why not give a fully freedom to run the simulation? In the md_umbrella.mdp, I set pull_k1=1000; pull_rate1= 0.0, but apparently, I am confused with pull_k1>0 combined with pull_rate1=0.

In my mdp, i set "none" to LINCS, because if I use "all-bonds", an error of "1099 constraints but degrees of freedom is only1074" occurs. 

Actually, there is no any window with a designed distance. Here I attach the histo.xvg, profile.xvg.

Thank you with regards,


On 5/22/12 9:36 AM, Du Jiangfeng (BIOCH) wrote:
> Dear Justin,
> Based on your questions to my simulation, I posted here yesterday hopefully
> it was the correct way to reply in this forum.

You've still replied to the entire digest message (which I've cut out); please
make sure to keep replies free of superfluous posts in the future.  The archive
is already pretty hopeless, but let's not make it worse :)

> In this morning I got a list of new windows of umbrella sampling, the overlap
> is sufficient enough, but I saw another problem:  In the histogram figure,
> the base of peak covers the distance of 2 nm instead of 0.2 nm., that's
> horrible! However, when I checked back to the simulation results of each
> window, the fluctuation of my pulled protein is only 0.4nm in maximum. So the
> base of peak shouldn't cover such long distance, right?

If the peaks aren't corresponding to the desired restraint distances, then there
are several potential problems:

1. Your restraints aren't set up the way you think they are (check grompp output
and .tpr file contents to be sure)
2. Your restraints are ineffectual (in which case you may need to revisit the
force constant)

I can't determine from your description what's going on.  What do you mean by a
maximum of 0.4 nm fluctuation?  In what quantity?  What do the contents of
pullx.xvg show you for the problematic window, and for that matter, the others?
  Are any of them producing the desired restraint distances?

Again I will ask you to share an image of the histogram and PMF profile; these
would be very helpful to see.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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