[gmx-users] trjconv

Marco Ceruso mceruso at physbio.mssm.edu
Mon Aug 25 19:33:02 CEST 2003

create an index.ndx file with mkae_ndx
then trjconv f traj.xtc -o prot.xtc -n index.ndx
this will prompt trjconv to read the index file and ask you which group you
want for output "Protein" in your case.
this will create prot.xtc a trajectory with the protein only

-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of Tanos
Sent: Monday, August 25, 2003 1:21 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] trjconv

	Hi folks,
	I have finished a MD simulation on a protein in a water box and now I
need to eliminate the water molecules from the .gro file in order to
perform the conformational analysis of the protein after MD. I am trying
to do this using trjconv but I am not having any success. Could someone
say me the right order of comands to use to eliminate the water
molecules and create a new .gro file having just the coordinates of the
the protein after MD ???? The information about this, from the manual,
is not clear for me.
	I am typing "trjconv -f 'filename.gro' -o 'newfilename'.gro" What am I
doing wrong ????????
	Thanks in advance.
	Tanos Celmar Costa Franca.
	IME - Rio de Janeiro - Brazil

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