[gmx-users] PBC correction to visualize a protein-membrane structure

Juan Munoz-Garcia juan.munoz-garcia at bioch.ox.ac.uk
Fri May 16 18:58:18 CEST 2014

Dear Justin,

thank you. I’ve tried the following but neither of them worked, I get the same result.

trjconv -f input.gro -o output.gro -s .tpr -trans 0 0  z_box/2 -pbc mol -ur compact

trjconv -f input.gro -o output.gro -s tpr -trans x_box/2  y_box/2  z_box/2 -pbc mol -ur compact

This is the last line of my input.gro file

19.51671  19.51671  13.80040   0.00000   0.00000   0.00000   0.00000   9.75836   9.75836

Juan C.

Your system was probably centered at z=0 instead of z = z_box/2 (commands used
for building the system would also help - I guess I should have been more
clear), hence it's getting split across PBC.  trjconv -trans in conjunction with
-pbc mol should be what you need.



Begin forwarded message:

From: Juan Carlos Munoz Garcia <juan.munoz-garcia at bioch.ox.ac.uk<mailto:juan.munoz-garcia at bioch.ox.ac.uk>>
Subject: Re: PBC correction to visualize a protein-membrane structure
Date: 16 May 2014 14:08:50 BST
To: <gromacs.org_gmx-users at maillist.sys.kth.se<mailto:gromacs.org_gmx-users at maillist.sys.kth.se>>

Thank you Justin,

please find a dropbox link to the image below.

I’ve used

trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole
trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact -center

and different combinations of those


Thank you.
Juan C.

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