[gmx-users] using VMD with GROMACS trajectories

Mark Abraham Mark.Abraham at anu.edu.au
Wed May 16 10:47:00 CEST 2007

sichuan xu wrote:
> Dear Mark and other friends£¬

In future, please change the subject of the email to something relevant, 
to improve your chances of getting a useful answer and avoid wasting 
people's time and effort.

> I am a new user of Gromacs. I can obtain .xtc, .top, and .log files. But 
> the gromacs installed here cannot view the .xtc file. So I used VMD to 
> view the .xtc file as suggested in the gromacs manual. To view the 
> trajectory by VMD, it needs two files, for an example, .psf and .dcd 
> files merged.
> If .xtc file is like .dcd file, what is like .psf file in gromacs?
 > How can I view the .xtc file with VMD?

Roughly speaking, a gromacs .top file has the same sort of information 
as a .psf file, but VMD won't read one natively. Instead, give VMD a 
structure file (.gro, .g96, .pdb or anything else) that corresponds (in 
the same order) to the atoms that are saved in your trajectory in place 
of the .psf file, and then load the trajectory (.trr or .xtc) into that 
molecule in the same way you would a .dcd file (see the VMD manual if 
you don't understand this step). VMD will guess the atom connectivity 
based on the original structure you give it - you should not expect this 
connectivity to correspond perfectly to that in your .top file.

The gromacs tool ngmx can do a rough and ready visualization, if the 
right X libraries exist and ngmx was installed. See "man ngmx" for info.


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