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?
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
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
