[gmx-users] Re: g_msd with input by trjconv -pbc nojump:a concern

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Mar 20 11:29:28 CET 2012

Hi Ioannis,

Coordinates are wrapped during the simulation because of efficiency.
There is no track kept of crossings of the boundaries. trjconv can
infer such crossings from sudden changes in the coordinates, larger
than half a box dimension. That means that for studying diffusion, you
have to make sure the sampling time and the box size are such that it
is impossible/unlikely that jumps on the order of half a box size
occur in the output trajectory.



2012/3/20 Ioannis Beis <ibeis at mail.student.oulu.fi>:
>> Message: 3
>> Date: Mon, 19 Mar 2012 15:05:43 +0100
>> From: Dommert Florian <dommert at 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 at gromacs.org>
>> Message-ID: <1332165943.4071.82.camel at 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: dommert at 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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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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