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

Justin A. Lemkul jalemkul at vt.edu
Tue May 22 13:40:50 CEST 2012

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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