lloyd riggs wrote:
-------- Original-Nachricht --------
Datum: Tue, 17 Apr 2012 07:49:06 -0400
Von: "Justin A. Lemkul" <jalem...@vt.edu>
An: lloyd riggs <lloyd.ri...@gmx.ch>, Discussion list for GROMACS users
<gmx-users@gromacs.org>
Betreff: Re: Questions
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.
http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette
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:
http://lists.gromacs.org/pipermail/gmx-users/2012-April/070528.html
Is this not the case?
No it worked for one, and I happily wrote that, then it didnt work for a single
other one?
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.
same way, using the .dat files with one single file and no error (it just
prints 0's for error if you try) and then make error or Standard deviation
analysis in excell or qti plot with all your histograms.
Well, I know you can do it, it just doesn't make much sense and I was trying to
rationalize what you were doing as a potential source of problem.
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.
I dont know. All I know is if I have it print one of the other deminsions, I
get the other curves mentioned.
When accusing the code of doing something wrong, "I don't know" isn't a very
good justification ;) The contents of pullx.xvg are the COM coordinates of the
reference group on the axis or axes along which the restraint was applied,
followed by the distance between the reference and pulled group, again along
each axis. In your case you should have the y-coordinate of the COM of the
reference, and dY, which represents the distance between the two groups along
the y-axis only. These values should be easy to confirm with g_traj and g_dist.
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.
So, A couple of them have almost all (90% of the 2000 points). If I do not
append the final data, they generate a curve that fits in the guasian. As soon
as I cut and paste the ends, it no longer works with the sam error mentioned.
So yes, its wierd to me. I even looked at the .txt file in a script editor and
there is nothing, no carriage no other things, same format as the rest, nothing
on the ends...so can not figure out how the software finds an error?
I even just looked at the code (just the reading and passing for lines
portions) and it still should not give an error even with some returns, or
other?
The only idea that comes quickly to mind is some problem with end-of-line
characters.
The couple I have that crashed early generate a curve but it looks complete
crap, pretty much looks like a bell really early?
The following couple of questions I asked are the most important ones, but you
haven't answered them. I won't be able to contribute anything else useful
without an answer to these.
-Justin
______________________
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
contents?
Further, a complete .mdp file (or at least the complete pull code section)
would
be useful.
-Justin
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.ll...@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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
Thank you for answereing,
I do sometimes post pretty quickly with problems, but something like this is
inigmatic and waste alot of time, and I know its something crazily simple. Its
just anoying as I was trying to keep to a standard for analysis.
SIncerely,
Stephan Watkins
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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