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[http://www.ks.uiuc.edu/Research/vmd/ VMD] is a molecular visualization program for displaying, animating, and analysing large [[Biological systems |biomolecular systems]] using 3-D graphics and built-in scripting.
'''VMD''' <ref>[http://dx.doi.org/10.1016/0263-7855(96)00018-5  William Humphrey, Andrew Dalke and Klaus Schulten "VMD: Visual molecular dynamics", Journal of Molecular Graphics '''14''' pp. 33-38 (1996)]</ref> is a molecular visualization program for displaying, animating, and analysing large [[Biological systems |biomolecular systems]] using 3-D graphics and built-in scripting. In addition to this VMD has a large array of extensions (see link below).
==Visualising a GROMACS trajectory==
Visualising a [[GROMACS]] trajectory:
 
first we produce a trajout.xtc file from the traj.xtc file, at the same time removing the [[periodic boundary conditions]]
 
:<code> trjconv -pbc whole </code>
 
then we load trajout.xtc into VMD:
 
:<code> vmd conf.g96 trajout.xtc </code>
==References==
==References==
#[http://dx.doi.org/10.1016/0263-7855(96)00018-5  William Humphrey, Andrew Dalke and Klaus Schulten "VMD: Visual molecular dynamics", Journal of Molecular Graphics '''14''' pp. 33-38 (1996)]
<references/>
==External links==
*[http://www.ks.uiuc.edu/Research/vmd/ VMD web site]
*[http://ftp.ks.uiuc.edu/Research/vmd/plugins/ VMD extensions page]
*[http://www.nvidia.com/object/vmd_on_tesla.html VMD on Tesla GPUs]
[[Category: Materials modelling and computer simulation codes]]
[[Category: Materials modelling and computer simulation codes]]

Latest revision as of 12:35, 2 April 2014

VMD [1] is a molecular visualization program for displaying, animating, and analysing large biomolecular systems using 3-D graphics and built-in scripting. In addition to this VMD has a large array of extensions (see link below).

Visualising a GROMACS trajectory[edit]

Visualising a GROMACS trajectory:

first we produce a trajout.xtc file from the traj.xtc file, at the same time removing the periodic boundary conditions

trjconv -pbc whole

then we load trajout.xtc into VMD:

vmd conf.g96 trajout.xtc

References[edit]

External links[edit]