[gmx-users] how to remove solvent molecules from xtc files

hayagreevan R smilidon at mail2Cool.com
Tue Apr 4 12:08:59 CEST 2006

hi all,
i am using this template of commands to remove the solvent molecules
from the xtc file.but i found that the solvent molecues are not being
deleted from the xtc file.The trajectory shows distorted image in vmd
when loaded on pdb file but works fine when loaded on .gro file which
also has solvent molecules.(either way of no use).All trajectories run
well on ngmx(with and without solvent molecules).
(procedure adapted as per a "reply" by Dr.Warren in the gromacs

trjconv_mpi -f viimd.trr -o viimd.xtc

make_ndx_mpi -f conf.gro -o index.ndx
(In this option i chose protein)

trjconv_mpi -f viimd.xtc -o ready.xtc -s 1BXL-bclxl-bak-complex.pdb -n

Can anyone please help me on this as I have some ten trajectory files
with the same problem.
Thanks in advance.

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