Hi Alan,
see Fig 3 in the paper I was mentionning in my previous post
(http://dx.doi.org/10.1063/1.2393240); from the legend the authors say
'deviation from linearity at long times is due to poor statistics'. So
to answer your question, that's probably true, most papers just show the
beginning of the plot where the MSD is linear. As quoted before by
David, one has just to take care about fitting in the linear region
(with the -beginfit and -endfit flags).
Cheers,
Patrick
Alan Dodd a écrit :
I've been playing with g_msd myself recently, and been seeing weird results
toward the end of the simulation. From the below post, it looks like I was
doing it correctly (apart from analysing the leaflets separately). Previous
posts in the mailing list have implied that increased noise towards the end of
a simulation is inherent in the algorithm, I just wanted to check that I was
interpreting those posts correctly? And if this is so, do people just not show
the results towards the end?
----- Original Message ----
From: David van der Spoel <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <[email protected]>
Sent: Wednesday, January 16, 2008 6:48:32 AM
Subject: Re: [gmx-users] About g_msd
Justin A. Lemkul wrote:
Hi Alan,
Thanks for the reply. My initial trajectory showed several of the lipids jumped
across the box and continued through the bilayer from there, which resulted in a
large displacement, so I processed the trajectory with trjconv -pbc nojump.
There is still a rather large initial displacement (within the first several
nanoseconds out of 100, likely due to my equilibration procedure of packing the
lipids tightly around the peptide), so I attempted to analyze the last 75 ns and
90 ns of the trajectory, using the structures at those times as the reference
(in g_msd -s). Still the same result, a large value of D.
Any ideas?
please go back to your original trajectory and do normal g_msd for the P
atoms only. (no mol flags etc.)
Thanks again.
-Justin
Quoting Alan Dodd <[EMAIL PROTECTED]>:
What happens if you visualise the trajectory? Two orders of magnitude in
scale of lipid movement should stick out like a sore thumb.
----- Original Message ----
From: Justin A. Lemkul <[EMAIL PROTECTED]>
To: [email protected]
Sent: Wednesday, January 16, 2008 12:27:45 AM
Subject: [gmx-users] About g_msd
Hello again,
I'm back with a few more questions about g_msd (version 3.3, in case I hadn't
mentioned that before). Thanks to Xavier's message earlier, I have abandoned
use of ordered trajectories to analyze my lipids. I will deal with lipid
"shells" in the future. For now I am approaching the problem of lateral
diffusion coefficients from a slightly different angle.
My system contains a helical peptide that is oriented asymmetrically with
respect to the DPPC bilayer. It is tilted and only partially embedded into
the
intracellular leaflet of the bilayer (at the beginning of the simulation).
Due
to the asymmetry, I would like to study the properties of the leaflets
separately, including, among other parameters, the lateral diffusion
coefficients of the component lipids.
I have found a few papers that have simulated pure DPPC bilayers, and am
using
them as somewhat of a reference point for the magnitude of the lateral
diffusion coefficients that I am determining: E. Lindahl and O. Edholm
(2001)
J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) Biophys.
J.
76.
For the top leaflet of my bilayer, I am getting a value of D =
(4.0+/-2.2)x10^-7
cm^2/sec (reasonable, in terms of order of magnitude, I think), but for the
bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec. I
figured
this enormous number was due to artefacts of PBC, so I tried every iteration
of
trjconv -pbc, but to no avail. Every result is quite similar. I tried
starting g_msd at a later time (10 ns, 25 ns) to determine if any large
initial
movements of lipids were responsible for the result, but I'm still coming up
with the enormous value of D (albeit slightly lower, ~200+/-400)
I am using g_msd -mol, with an index file that contains molecule numbers, and
then using g_analyze on the output .xvg file to get the values of D.
Has anyone ever experienced anything similar? Am I missing something
obvious?
Thanks in advance, as always, especially if you read the entirety of my
lengthy
message.
-Justin
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
____________________________________________________________________________________
Never miss a thing. Make Yahoo your home page.
http://www.yahoo.com/r/hs
_______________________________________________
gmx-users mailing list [email protected]
http://www.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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
_______________________________________________________
Patrick FUCHS
Equipe de Bioinformatique Genomique et Moleculaire
INSERM U726, Universite Paris 7
Case Courrier 7113
2, place Jussieu, 75251 Paris Cedex 05, FRANCE
Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30
E-mail : [EMAIL PROTECTED]
Web Site: http://www.ebgm.jussieu.fr/~fuchs
_______________________________________________
gmx-users mailing list [email protected]
http://www.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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
