[gmx-users] remove periodic boundary in tpr file

[tangxuan]

I try to remove the periodicity to get a new .xtc file and one .gro
file. The commands are shown below:
"trjconv -f original.xtc -s original.tpr -n index -o frame_0.gro -dump 0
-pbc nojump"

 "trjconv -f original.xtc -s original.tpr -n index -o new.xtc  -pbc
nojump"
When I use g_rms to calculate the rmsd by new .xtc and .gro file, there
is a warning and other things goes well. Command i used is "g_rms -f
new.xtc -s frame_0.gro -o  rmsd.xvg" and the warning is "can not make
broken molecules whole without a run input file,don't worry, mdrun
doesn't write broken molecules". I think i have removed the boundary,
and why it says there is an broken protein?

Thanks.

Jiaowei Tang



On Thu, 2007-10-04 at 10:16 +0200, Tsjerk Wassenaar wrote:
> Hi Jaowei Tang,
> 
> Better use a .pdb or .gro file. Maybe the starting structure (obtained
> after running pdb2gmx)?
> By the way, if you removed the jumps over the boundary (you don't
> really want to remove periodicity :p) you must already have a proper
> structure. Or you can then extract the first frame from the trajectory
> and use that as the starting point. 
> 
> Tsjerk
> 
> On 10/4/07, tangxuan <tangxuan82 at gmail.com> wrote:
>         Dear all,
>         I am try to use g_rms to a protein, but its start structure in
>         the
>         simulation is not in one box. I removed the periodicity for
>         the xtc file
>         by trjconv, but do not know how to remove the periodicity in
>         the tpr 
>         file. Could you give me some suggestions?
>         
>         Thank you.
>         
>         Jiaowei Tang
>         
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> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center 
> Utrecht University
> Padualaan 8 
> 3584 CH Utrecht
> The Netherlands
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