On Tue, 2012-03-20 at 11:38 +0200, Ioannis Beis wrote: > > 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.
Hi, I would not use nojump, because g_msd seems to deal with this correctly, but -pbc whole, perhaps this can solve this problem. /Flo > 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 > > -------------- next part -------------- > > A non-text attachment was scrubbed... > > Name: not available > > Type: application/pgp-signature > > Size: 198 bytes > > Desc: This is a digitally signed message part > > Url : > > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120319/bf0fbf11/attachment-0001.bin > > > -- 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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