Message: 3
Date: Mon, 19 Mar 2012 15:05:43 +0100
From: Dommert Florian <domm...@icp.uni-stuttgart.de>
Subject: Re: [gmx-users] g_msd with input by trjconv -pbc nojump:a
concern
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <1332165943.4071.82.camel@fermi>
Content-Type: text/plain; charset="utf-8"
Hi and thanks for the reply!
Hi,
perhaps this problem is related to bug 774:
http://redmine.gromacs.org/issues/774
The destination exhibits internal server error, thus I don't have access.
which has been discussed quite often, recently. Somehow there is a
problem in the order of removing the PBC and jumps. As already
mentioned, I could solve the problem by providing a trajectory with
whole molecules to g_msd. An indexfile with seperate groups for every
molecule has to be created and finally every single molecule group has
to be analyzed, but WITHOUT the -mol flag. Afterwards the resulting MSDs
only need to be averaged.
I used trjconv first with nojump and I used this as input for a
subsequent trjconv with mol. I suppose that's what you mean by
"providing a trajectory with whole molecules to g_msd". Then I issued
g_msd without -mol, providing as index all the atoms of the under
interest molecule. The results are still bad. Am I doing something
wrong still?
Apart from this (which is an additional concern as it seems), my
initial question was mostly about whether or not .xtc files carry all
information about jumps in addition to coordinates. If the frequency
of saving is small, then it might be possible for a molecule to be in
two consecutive frames whole, but in the inbetween time it might have
jumped. Can trjconv -pbc nojump capture this event? Or is it aware
only if it sees the molecule crossing at the very moment of the frame?
If the second case is true, then this can have fatal consequencies to
MSD calculations. An extreme example: if a molecule moves along 1D in
a box that has corresponding vector of length a and between two frames
moves by a, then one case gives rise to displacement of a and the
other of 0.
I would appreciate if someone let me know whether -pbc nojump
continuity is unconditional or frequency of saving-dependent.
Thank you in advance!
Best regards,
Ioannis
/Flo
On Mon, 2012-03-19 at 14:31 +0200, Ioannis Beis wrote:
Dear Gromacs users,
I have been trying to calculate the lateral MSD of lipid molecules
within a bilayer. I have performed simulations in a rectangular box
with PBC. I have used trjconv with -pbc nojump. I compared results
between the initial trajectory and the one generated by trjconv for 6
different lipids. In 5 cases the calculated MSD was identical and only
in one there was difference (big difference). According to the
results, MSD loses linearity and exhibits large fluctuations after
some point. The above give rise to the following concern.
As far as I understand, -pbc nojump checks if any molecule crosses the
box boundaries and if yes it brings back the broken part from the
symmetric side to the original place, keeping the molecule whole. This
way box information is lost, but each molecule is supposed to have
continuous trajectories. The true continuity of trajectories, however,
is only secured only if .xtc files carry all information of boundary
crosses based on the time step of the initial run in addition to all
coordinates for all times. Otherwise, the result is clearly dependent
on the frequency of saving and continuity is not guaranteed.
E.g. in my case -I have small frequency of saving (100 ps) for long
simulations to avoid very large output files- one can't tell based
merely on the coordinates whether or not a lipid crossed boundaries
between two consecutive frames. Of course if the lipid went back and
forth then the result of the calculation would not be affected but
only by statistical means; however if the lipid had an overall
translation across the box (not captured by -pbc nojump because the
molecule is whole in both frames), then the calculation is destroyed.
If this is the case, it seems to me that g_msd might in practice give
correct results for proteins, but for smaller molecules the
reliability of the results depends sensitively on molecule
size-frequency of saving coordinates relationship and might give rise
to huge systematic errors.
Is there a way to obtain a converted trajectory that guarantees
unconditional continuity, so that one makes sure that he obtains the
proper MSD for his molecules?
Thank you in advance!
Best regards,
Ioannis
--
Florian Dommert
Dipl. - Phys.
Institute for Computational Physics
University Stuttgart
Pfaffenwaldring 27
70569 Stuttgart
EMail: domm...@icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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