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.bsbi...@iiu.edu.pk
<mailto: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
<mailto: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
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
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
