[gmx-users] Re: Questions

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 17 13:49:06 CEST 2012

lloyd riggs wrote:
> Dear Justin,
> So I get no answere on the mail list so decided to ask you (and most likely
> Dr. Abrahams if you dont answere) some questions as follows.

Please keep all discussion on the mailing list.


Your problems are still rather inexplicable to me (hence why I didn't reply), so 
I'll ask a few questions and perhaps someone else will have an idea or I'll 
stumble upon it based on your answers.  I assumed as of this morning that this 
issue was solved:


Is this not the case?

> So my experience with Umbrella and WHAM up untill now,
> I followed the tutorial and a paper using similar proteins which worked well.
> I did make one slight change in the pull code for the ki 2000 (set by a paper
> with the similar proteins) changing to 2500 kCal/mol over 4 ns.  Basically
> the internal code does something where you have to have two seperate values
> or the written dhdl always equals zero due to the equation in the code.
> In an case, I did this twice and generated models for an NPT equilabrated
> system, with and without a small molecular complex as well generating evenly
> spaced models across a 4 ns run each (before the pull code).  I then cliped
> the first and last for two sets, and chose 10 randomly spaced models in there
> for each with and without (20 total)
> I then production ran these with a rather complicated index file as to later
> pull out the contributions energy wise to the overall effects of things.  I
> had done this already by hand for one run not included here and was able to
> get relativly decent figures by summing energies and pluging these into
> standard thermo equations (neglecting obviously some contibutions so relative
> but fitting wet laboratory eqperimental error so still good).
> So, I then now have 10 and 10 pullx, pullf, and tpr (along with energies,
> etc...).  I started to look at each one individually using WHAM to compare
> the profiles and found the following.

How can you use individual files as input into WHAM?  By necessity, the 
algorithm works by assembling multiple files.

> As I used a N Y N (my origional axis were on the Y rather than the Z as they
> were arbitrarily generated) and found the pullx.xvg files write out the
> coordinates for the wrong position, but these can be found using other

How so?  I have never seen this happen.

> gromacs tools.  Still when I use these the end results (energy calculated at
> time 0 and end) are correct, but there is just a jump half way through the
> run from a low to high point, but no curve)

I'm not clear on what you mean here.

> For the pullf.xvg files (individually), I went through and found only the
> runs where there was no interuption (where I didnt have to start from a .cpt
> file) the WHAM takes the files and generates nice curves which vary only
> slightly as expected.  However any run where the pullf.xvg was interupted and
> then continued as pullf.part0001.xvg etc...) and I cut and pasted the ends
> into another full pullf.xvg file it cant find the proper columns.  Example.

That seems very weird.  These are simple text files; if pasted together properly 
I see no reason why their interpretation should be flawed simply by appending 
them with a text editor.

> ______________________
> Only 2 columns on line 2012 in file pullf_14.xvg Only 2 columns on line 2013
> in file pullf_14.xvg

Can you post what these lines are?

> ------------------------------------------------------- Program g_wham_d,
> VERSION 4.5.5 Source code file:
> /tmp/var-tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/tools/gmx_wham.c,
> line: 1805
> Fatal error: Found 1 pull groups in traj_14.tpr, but 2 data columns in
> pullf_14.xvg (expected 1)
> Maybe you confused options -ix and -if ?

Is this a possibility?  Are your files named correctly with respect to their 

Further, a complete .mdp file (or at least the complete pull code section) would 
be useful.


> For more information and tips for troubleshooting, please check the GROMACS 
> website at http://www.gromacs.org/Documentation/Errors 
> -------------------------------------------------------
> When I feed it just the column for the energies, it then say it expects
> another column?
> I looked at things just to see if there were hidden marks or something, and
> con not figure out why it wont take the files.  Theres no hidden marks,
> spaces or anything?
> In any case, I now have all these files and need to figure out why I have
> such a wierd error.  I should note, the way our software was compiled on the
> Linux cluster doesnt allow any append options or I would have just done that
> in the first place.
> Sincerely
> Stephan P. Free Watkins stephan.lloyd at students.unibe.ch University of Bern 
> Insel Spital RIA Sahli Haüs II Freiburstrasse 21 Bern 3011


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


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