[gmx-users] 2 beginner?s questions

Maxim Fedorov maxim.fedorov at ucd.ie
Tue May 16 18:13:09 CEST 2006

Message: 6
Date: Tue, 16 May 2006 23:02:15 +1000
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] 2 beginner?s questions
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4469CD57.1070307 at anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Sampo Karkola wrote:
> Hi,
> also VMD is quite handy. You'll need pdb's for VMD, too.

Not true. VMD eats at least .gro, .g96, .trr and .xtc as well as .pdb
and a whole pile of others.
Indeed - VMD takes every gromacs formats
Just take care about the terminal residials - sometimes VMD doesn't
treat them properly.
In this case just use the 'atomselect' option to select the whole
molecule for a reperesentation/analysis (via the atom indexes).
It is also a good idea to remove periodicity (with gromacs tools) 
BEFORE analysing your trajectory with VMD.
But as a whole - the VMD could be a good choice.



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