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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Chandan kumar Choudhury NCL, Pune INDIA
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