Sarah Witzke wrote:
-----Original Message----- From: gmx-users-boun...@gromacs.org on behalf of
Justin A. Lemkul Sent: Thu 19-11-2009 02:09 To: Gromacs Users' List Subject:
Re: SV: SV: SV: [gmx-users] Hydrogen bonding
Sarah Witzke wrote:
Sarah Witzke wrote:
<snip>
ARRGH, I'm sorry, things went too quick :-( So the lifetime in average
per hbond is 628.571 ps?
Yes, per the calculation. For a bit more about the analysis, see the
"Please read and cite" notices, as well as this thread:
http://lists.gromacs.org/pipermail/gmx-users/2009-February/039955.html
The note about the correlation function would imply that the correlation
function itself has not converged until its value is < 0.001. This is
usually a result of insufficient data, either the length of the
simulation, or number of frames analyzed (based on the spacing of the
frames).
Hmm, so using 120 ns simulation from a standard .xtc file (timestep of 10
ps) is not long enough. Perhabs I should try the original .trr file...
The .xtc file I'm using only contains DMPC and the small molecule, no
solvent - I can't see this would make a difference in this case, am I
right?
The correlation will depend on how much the interactions are changing over
the period you analyzed. If you are analyzing a small molecule and DMPC,
water should not matter.
I have now tried with the full length (220 ns) .trr file and the -ac output
still prints a warning:
ACF 106/106 Normalization for c(t) = 1.23261 for gh(t) = 5.58815e-05
WARNING: Correlation function is probably not long enough because the
standard deviation in the tail of C(t) > 0.001 Tail value (average C(t)
over second half of acf): 0.000172327 +/- 0.00277407
In your opinion, does this mean that I cannot trust the value of the
lifetime, since the correlation function is not converging?
I'm not entirely sure. Please see the posts from David in the thread I
referenced before about some potential issues with the ACF in the g_hbond
calculation. I assume you are using version 4.0.x?
I'm using version 4.0.4 for consistency. I have read the posts from you and
David van der Spoel
(http://lists.gromacs.org/pipermail/gmx-users/2009-February/039955.html) as
well as the article given by g_hbond. I guess this auto correlation function
and the lifetime derived by this is... well, I'm not sure I trust it enough
to put it in a paper - especially since my acf doesn't converge (which I
still find strange, it should not matter that I have only saved coordinates
every 10 ps in my .trr file when using the Luzar acfs-approached, right?).
The - hbm option i g_hbond creates a matrix that can be converted to a .eps
file by usin xpm2ps. The picture obtained is nice looking but lacking in some
of the information I would like to derive. I would like to know how many
frames each hbond exists (another way to consider lifetime). I have opened
the .xpm file in a text editor and there are a long list of lines starting
similar to tgis one: /* x-axis: 100000 100010 100020 Can I somehow obtain
the number of frames for each hbond from this?
Either write a script that counts the number of instances of "o" characters per
line in the .xpm file, then divide by the total number of frames, or iteratively
call g_hbond for each of the H-bonds that were initially identified (and whose
indices are now written to hbond.ndx from -hbn). The latter approach will still
require some post-processing, of course, since each output .xvg file will be a
series of either 0 or 1, indicating the absence or presence of that particular
H-bond.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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/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/mailing_lists/users.php
