[gmx-users] getting rid of PBC, completely

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jan 19 13:46:15 CET 2012 

On 19/01/2012 11:27 PM, Chandan Choudhury wrote:
> On Thu, Jan 19, 2012 at 3:49 PM, Tsjerk Wassenaar <tsjerkw at gmail.com 
> <mailto: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).

The origin is always at (0,0,0) by definition, not by the contents of 
fr.box. There's no magic center of a periodic box, either.

fr.box has the box dimensions, which in general require more than the 3 
pieces of information required for a rectangular solid box.

> 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?

For some box types, yes.

Mark

>
>
>     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 <mailto:iitdckc at gmail.com>> wrote:
>     >
>     >
>     > On Thu, Jan 19, 2012 at 12:17 PM, Mark Abraham
>     <Mark.Abraham at anu.edu.au <mailto: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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>     <mailto:gmx-users at gromacs.org>
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>     >
>     >
>     >
>     >
>     > --
>     > Chandan kumar Choudhury
>     > NCL, Pune
>     > INDIA
>     >
>     >
>     > --
>     > gmx-users mailing list gmx-users at gromacs.org
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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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>
>
>

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