Hello,
It's possible to convert to a single pdb file containing all the frames
using:
trjconv -f cpeptide_md.trr -o trajout.pdb -s cpeptide_md.tpr
You can then load it into pymol using:
pymol trajout.pdb
And it will load all the frames.
If you render a movie into png you will have lots of *.png files, which
you can convert into a movie using the following command:
convert *.png ppm:- | ppmtoy4m | yuvscaler -O SVCD | mpeg2enc -f 3 -b
4500 -q7 -o mpegfile.m2v
For this you need imagemagick (convert) and mjpeg-tools (rest)
I've just started out doing some MD simulations and I was trying to use
pymol to see the simulations (vmd is more widely used for this) and this
is what I've came up so far. Next I will need to make a pymol script to
automatically render the png files, preferably without running X as my
number crunching box isn't even connected to a monitor.
Best,
BA
Tsjerk Wassenaar wrote:
Hi Yunfeng Hu,
Frankly, with Pymol, people don't as far as I know. What I usually do is
determine for the first frame of the individual pdb files (obtained with
trjconv -sep) the orientation, viewing point and appearance. This I save
in a .pml script. Then with a bit of python code, looping over the
frames, calling them, processing the script, raytrace, write the image
and delete the object again. It's at present the best I can think of. It
appears that Dino is capable of processing a gromacs trajectory and
outputting raytraced frames, but I haven't felt like starting at the
bottom of that learning curve...
To help out a bit, the loop code could look like this:
for i in range(nr_of_frames):
cmd.load('frame_' + repr(i) '.pdb', 'prot')
cmd.do('@script.pml')
cmd.delete('prot')
Everything to go in script.pml could ofcourse also be explicitly given
in the loop...
Hope it helps,
Tsjerk
Yunfeng Hu wrote:
Hi, I wonder if people can give a summary of how pymol makes movies
out of gromacs trr (or xtc) files without having to use all the
individual frame pdb files. Thanks!
Eric
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