On Thu, Jan 19, 2012 at 3:49 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
> Hi Chandan, > > The box is accessible from the t_trxframe struct. Assuming you have > > t_trxframe *fr > > You can access it through > > fr->box > Thanks Tsjerk. It (fr.box) did help me to get the box coordinates. fr.box[XX][XX], fr.box[YY][YY] and fr.box[ZZ][ZZ] gives me the values but fr.box[XX][YY], fr.box[XX][ZZ] prints 0. Which seems to me that the origin of the box is at (0,0,0). Then, fr.box[XX][XX] is the maximum X-coordinate, fr.box[YY][YY] is the maximum Y-coordinate,fr.box[ZZ][ZZ] is the maximum Z-coordinate. Am I correct? > But if you remove jumps first, you're fine anyway. Just don't put > things back in the box afterwards. And don't center if your aim is > calculating MSDs. > Yeah, you are right. Chandan > > Hope it helps, > > Tsjerk > > On Thu, Jan 19, 2012 at 11:14 AM, Chandan Choudhury <iitd...@gmail.com> > wrote: > > > > > > On Thu, Jan 19, 2012 at 12:17 PM, Mark Abraham <mark.abra...@anu.edu.au> > > wrote: > >> > >> On 19/01/2012 5:39 PM, Chandan Choudhury wrote: > >>> > >>> > >>> Dear gmx-users, > >>> > >>> I have a simulated a system containing a linear polymer in a cubic box > >>> with water molecules. I need to get rid of PBC effect on the system > such > >>> that I can execute my own analysis code. I intend to compute the msd of > >>> water molecules along the polymer backbone. > >> > >> > >> You can't "get rid of PBC", you can only manage it. The question reduces > >> what you want to see if a molecule diffuses across the periodic boundary > >> from near one end of the polymer to the other end. > >> > >> > >>> So, when I execute my own analysis code, I see the msd's are abrupt > (i.e > >>> very high), this is due to the pbc. So, for getting rid of PBC effect, > I > >>> performed the suggested trjconv workflow > >>> ( > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > ). > >>> > >>> Below are my executed commands : > >>> > >>> # Made the system whole > >>> > >>> echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc whole -o > >>> 0-4_whole.xtc > >>> > >>> # 0 is the whole system. md0-4.tpr is the initial tpr file containing > >>> whole (no broken) polymer inside the cubic box. > >>> # Extracted 1st frame from the initial trajectory > >>> > >>> echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc nojump -o 1st.pdb > >>> -dump 0 > >>> > >>> # used the whole trajectory to remove jumps with reference to the 1st > >>> frame. > >>> echo 0 | trjconv_4.5.5 -s 1st.pdb -f 0-4_whole.xtc -pbc nojump -o > >>> 0-4_nojump.xtc > >> > >> > >> So here you said "let molecules diffuse away from the solute". > >> > >> > >>> > >>> #system is being centered > >>> echo "0 0" | trjconv_4.5.5 -s md0-4.tpr -f 0-4_nojump.xtc -o > >>> 0-4_center.xtc -center > >>> > >>> #putting every atom in the box > >>> echo 0 | trjconv -s md0-4.tpr -f 0-4_center.xtc -o 0-4_box.xtc -pbc > atom > >> > >> > >> ... and now you said "take all the atoms and put them back in the box", > >> creating jumps whenever one crosses the boundaries. > >> > >> > >>> > >>> Still when I execute my analysis code, I do see the abrupt behaviour in > >>> the msd plot. Can someone guide me how to completely get rid of PBC > >>> artifacts. > >> > >> > >> Don't simulate with them :-P Is your analysis technique sound for the > >> periodic case? > > > > > > No, my analysis code doesnot take care of PBC. As to deal with PBC, I > need > > to have the box vectors (for atleast NPT simulation) from the trajectory > and > > I am unable to extract the box vectors (as of date). > > > > Chandan > > > >> > >> > >> Mark > >> > >> -- > >> 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/Support/Mailing_Lists/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/Support/Mailing_Lists > > > > > > > > > > -- > > Chandan kumar Choudhury > > NCL, Pune > > INDIA > > > > > > -- > > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > > > > -- > 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 > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists >
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