[gmx-users] problems about trjconv

[Justin A. Lemkul]

Quoting Di Pan <dpan at uab.edu>:

> Hi, All
>
> I do my md simulation for 30ns, but after 20ns the protein move out of
> the box, so it seems that the protein is broken in .trr file. I try to
> use trjconv to put the protein back into the box and make the protein
> whole. The command is like below:

Read here:

http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions

If the protein is just "diffusing out" of the box, there is no problem.  If
however, the protein "breaks," then there's likely a problem with your
topology, but you are likely just seeing an effect of PBC.

-Justin

>  trjconv trjc -f *.trr -o out.trr -s *.tpr -pbc nojump -center rect
>
> But after run the trjcov command, some parts of the protein is till out
> of box, and seems like broken.
> Is there anyone meed the same problem can tell me how to resolve this
> problem.
>
> Thank you very much
>
> Di,Pan
>
> Di,Pan
>
>
>



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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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