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 chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Dec 8, 2011 at 10:56 AM, Saba Ferdous <saba.bsbi...@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 > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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