[gmx-users] I want only coordinates in md.xtc/md.pdb

[Mark Abraham]

On 8/12/2011 5:04 PM, Chandan Choudhury wrote:
> For any text file, use your favorite editor to delete all your water 
> molecules. It will load very fast. For the xtc/trr files, use trjconv 
> with an index file to write a new xtc/trr file without water 
> molecules. Index file should contain the atom nos. of the molecules 
> you want.
>
> trjconv -s a.tpr -f a.xtc/trr -n a.ndx -o b.xtc/trr

Indeed, and the OP may wish to consider the advice here 
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume

Mark

>
> chandan
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> On Thu, Dec 8, 2011 at 10:56 AM, Saba Ferdous <saba.bsbi154 at iiu.edu.pk 
> <mailto:saba.bsbi154 at iiu.edu.pk>> wrote:
>
>     Dear Sir,
>     I need to ask you that if I want only pdb coordinates in the
>     resultant md-noPBC.xtc/md-noPBC.pdb file rather than the solvant
>     atoms and coordinates then what should I do. because the water box
>     causes very delay in loading of frames and its difficult to
>     viualize the trajectory. kindly help me to get out of the broblem.
>     I only want that my protein get display in vmd rather than the
>     water box.
>     the size of md-noPBC.xtc is 612 Mb
>     md-noPBC.pdb  is 13.2 GB
>
>     analysis is getting very slow and system is hanging. kindly help
>     me out to fix this problem.
>
>     Regards
>     Thanks
>
>
>     -- 
>     Saba Ferdous
>     Research Scholar (M. Phil)
>     National Center for Bioinformatics
>     Quaid-e-Azam University, Islamabad
>     Pakistan
>
>
>     --
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