[gmx-users] getting rid of PBC, completely

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jan 19 07:46:36 CET 2012

Hi Chadan,

You should stop after your second step, removing jumps. Don't center.
And definitely don't put the system in the box, as that exactly undoes
removal of jumps.



On Thu, Jan 19, 2012 at 7:39 AM, Chandan Choudhury <iitdckc at gmail.com> 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. 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
> #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
> 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.
> Chadan
> --
> Chandan kumar Choudhury
> NCL, Pune
> --
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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

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