[gmx-users] Re: rerun of trajectory

Paul Barrett barrett at biop.ox.ac.uk
Thu May 15 10:36:01 CEST 2003

is it solvated? Can you remove the water and just view the other stuff?
This reduces my files by 80-90% in size.

if so....
1) generate an index file with an entry "not water" as follows..

make_ndx -f (file name e.g. the .pdb or .gro that you started the
simulation with)

then find the SOL entry e.g. "15". Type !15 [return]. This should
generate a new entry called !SOL (i.e. not sol). Exit make_ndx by typing

3) use trjconv with the index file you have just made...e.g

trjconv  -f main.xtc -s post_pr.tpr -o nowater.xtc -n index.ndx -pbc

It would also be worth converting the trajectory to one with fewer


>actually the trr file is about 5.3G.its really huge as i have
>saved the velocities every 0.2ps.also i ran the tpbconv command from the
>same dir which has the .trr file.But it still does not seem to recognize
>will increasing the number of steps after which the velocities
>are written help me decrease the size,say after every 10 or 15ps.
>i have a feeling the huge memory size of 5.3.g for only 1ns seems to be giving
>me the trouble. i'm unable to view the movie also in VMD.Also my system is
>quite huge,about 22500 atoms.
>Is anyone aware of any software that can help me view a trajectory file of
>about 5-6GB.
>Swetha Vijayakrishnan
>Project Assistant
>C/O Dr.Shekhar.C.Mande
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