[gmx-users] Re: Umbrella sampling question

[Gmx QA]

Hi Chris

Seems my confusion was that I assumed that the distances in the
profile.xvg-file should correspond to something I could measure with
g_dist. Turns out it does not.
Thank you for helping me sorting out this, I got it now :-)

About pull_pbcatom0 though. My box is >> 2*1.08 nm in all directions:
$ tail -n 1 conf0.gro
  12.45770  12.45770  17.99590

I am still not sure what pull_pbcatom0 does. You said it should not have
any effect on my results, but changing it does result in a different
initial distance reported by grompp.

In my initial attempts at this, I did not specify anything for
pull_pbcatom0, but in the grompp output I get this

Pull group  natoms  pbc atom  distance at start     reference at t=0
       0     21939     10970
       1         1         0   2.083                 2.083
Estimate for the relative computational load of the PME mesh part: 0.10
This run will generate roughly 761 Mb of data


Then, following the advice in the thread I referred to earlier, I set
pull_pbcatom0 explicitly in the mdp-file to be an atom close to the COM of
the Protein. Then I get from grompp

Pull group  natoms  pbc atom  distance at start     reference at t=0
       0     21939      7058
       1         1         0   1.808                 1.808
Estimate for the relative computational load of the PME mesh part: 0.10
This run will generate roughly 761 Mb of data

As you can see, the initial distance is different (2.083 vs 1.808), and
1.808 is the same as the distance reported by g_dist. Do you have any
comments here as to why this is?

Thanks
/PK


What you reported is not what you did. It appears that grompp, gtraj, and
g_dist report the same value.
Please also report the value that you get from your pullx.xvg file that you
get from mdrun, which I suspect
will also be the same.

The difference that you report is actually between the first FRAME of your
trajectory from g_dist
and the first LINE of the file from the g_wham output. I see no reason to
assume that the values in the
output of g_wham must be time-ordered. Also, I have never used g_wham
myself (I use an external program
to do wham) and so I can not say if you are using it correctly.

My overall conclusion is that you need to investigate g_wham output not
worry about a new run at this stage.

Regarding pull_pbcatom0, there is lots of information on the mailing list
about this. It is a global atom number
that defines the unit cell for selection of which periodic image of each
molecule will be used for the pulling.
If all of your box dimensions are >> 2*1.08 nm, then pull_pbcatom0 will not
affect your results.

Chris.