[gmx-users] using VMD with GROMACS trajectories
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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