[gmx-users] getting rid of PBC, completely

[Chandan Choudhury]

On Thu, Jan 19, 2012 at 3:49 PM, Tsjerk Wassenaar <tsjerkw at 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 <iitdckc at gmail.com>
> wrote:
> >
> >
> > On Thu, Jan 19, 2012 at 12:17 PM, Mark Abraham <Mark.Abraham at 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
> >>
> >> --
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> >
> >
> >
> >
> > --
> > Chandan kumar Choudhury
> > NCL, Pune
> > INDIA
> >
> >
> > --
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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
> --
> gmx-users mailing list    gmx-users at gromacs.org
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