[gmx-users] Some basic questions about trajconv

ERASTOVA V. valentina.erastova at durham.ac.uk
Wed Jul 2 12:00:04 CEST 2014


trjconv is a very versatile tool.

if you do trjconv -h it will tell you:

Option -center centers the system in the box. The user can select the group
which is used to determine the geometrical center. Option -boxcenter sets the
location of the center of the box for options -pbc and -center. The center
options are: tric: half of the sum of the box vectors, rect: half of the box
diagonal, zero: zero. Use option -pbc mol in addition to -center when you
want all molecules in the box after the centering.

I think you need to use command -center in conjunction with -pbc. For -center select your group of atoms and for the whole trjconv you will need to select no-water option.

You have to play around to see what will give you necessary result. You possibly would need to iterate the trjconv over: 1st remove water, then centre atoms.


On 2 Jul 2014, at 10:23, gromacs.org_gmx-users-request at maillist.sys.kth.se<mailto:gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:


Message: 1
Date: Wed, 2 Jul 2014 12:52:32 +0800
From: Yip Yew Mun <yipy0005 at gmail.com<mailto:yipy0005 at gmail.com>>
To: gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>
Subject: [gmx-users] Some basic questions about trajconv
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Hi all,

I?ve recently switched from AMBER and started using Gromacs. I have just ran a CG MD and I wish to do post-analysis on the trajectory. So if I wish to center my molecule in the water box, then remove the waters, what should the appropriate command for trajconv be?

Thanks, any help would be greatly appreciated. =)

Yip Yew Mun (Mr) | PhD Research Scholar | Division of Chemistry & Biological Chemistry
School of Physical & Mathematical Sciences | Nanyang Technological University | Singapore 639798
Tel: (+65) 97967803 | Email: yipy0010 at e.ntu.edu.sg<mailto:yipy0010 at e.ntu.edu.sg> | GMT+8h

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