[gmx-users] Re: Re: Re: Re: umbrella potential

[Stefan Hoorman]

2009/9/26 <gmx-users-request at gromacs.org>

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> Stefan Hoorman wrote:
>
> > Well, I tried again, this time simulating 1ns each window. I thought
> > about simulating more, but thought of making a test before making longer
> > simulations for nothing. And again, my histogram looks like a
> > chromatographic peak, but the range this time is different. The rest of
>
> You should have overlapping roughly Gaussian distributions.  I can't tell
> if
> that's what you have, or if you have independent peaks.  If the latter is
> the
> case, then your windows do not overlap sufficiently to run WHAM.
>
> > the histogram is a straight line parallel to the x axis set in zero. I
>
> Parallel lines indicate discontinuities in the WHAM analysis.  I really
> think
> you need to post an image of this online so we can see.  Without seeing
> what
> you're dealing with, it's very hard to be helpful.
>
> > didn't understand what you meant by "getting what you think you are
> > setting up". I have checked the distance between my groups, both with
> > g_dist and by visual aid. The separate all right, there is no doubt
> > about that. Each window is what it should be, a window for the 1.5nm
> > distance starts at 1.5, decreases a little bit in the first picoseconds
> > and then stabilizes at 1.47 or 1.45. When I start g_wham analysis, the
> > verbose states that my initial distance is 0.99nm and then it says that
> > "Determined boundaries to 1.046511 and 2.140948". I tried this time
>
> Right, because your windows appear to range between these two values, so
> the
> closest window is restraining your structures at roughly 1 nm, and the
> furthest
> window is restraining the strucutres at 2.14 nm COM separation.  Is this
> what
> you expect?  I thought before you were dealing with distances out to 2.5
> nm.
>
> > simulating longer periods, and got the same result as before. The
> > profile graphic stars as a descending curve from 0 to -5 kCal, then it
> > starts rising in a "up the hill" way until it reaches +45kCal. I really
> > don't know what I am doing wrong this time.
> >
>
> Can you re-post the .mdp options you're using for pulling?  Also, images of
> both
> your histogram and profile would be extremely helpful.  I'm having a hard
> time
> picturing what you're describing with respect to the histograms.
>
> -Justin
>
Ok Justin, here are both profile and histogram files. Please let me know if
you can't get access or something like this. I have never used this
protobucket before.
"http://i784.photobucket.com/albums/yy123/stefhoor/wham_stefhoor/profile.jpg
"
"
http://i784.photobucket.com/albums/yy123/stefhoor/wham_stefhoor/histogram.jpg
"
And here are my pull code stuff that is inside my mdp files. The first one
(Pull Code 1) is the one I used to separate the structures, and the
following (Pull Code 2) is the one used to simulate each window.
; Pull Code 1
pull  =  umbrella
pull_geometry  =  distance
pull_dim  =  Y Y N
pull_nstxout  =  10
pull_nstfout  =  1
pull_ngroups  =  1
pull_group0  = Protein
pull_group1 = SLC
pull_vec1  =  1 1 0
pull_init1  =  0
pull_rate1  =  0.001
pull_k1  =  2000
pull_constr_tol  =  1e-06
pull_pbcatom0  =  0
pull_pbcatom1  =  0

; Pull Code 2
pull  =  umbrella
pull_start  =  yes
pull_geometry  =  distance
pull_dim  =  Y Y N
pull_nstxout  =  10
pull_nstfout  =  1
pull_ngroups  =  1
pull_group0  = Protein
pull_group1 = SLC
pull_vec1  =  1 1 0
pull_init1  =  0
pull_rate1  =  0
pull_k1  =  2000
pull_constr_tol  =  1e-06
pull_pbcatom0  =  0
pull_pbcatom1  =  0

The rest of my mdp stuff is pretty standard so, to save space I didn't post
it, but if you think it is necessary I would be glad to post it as well.
Sorry about the distance, I inverted the 2.41 (wrote 2.14). My separation is
from starting position (close to 1nm) till 2.5. But since the structures
always move a little in the beginning of each window, I guess the final
maximum distance is 2.41.
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