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如何把lammps的轨迹文件转化为视频呢？已有2人参与
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2楼2014-01-11 00:17:13
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------- To view a lammps trajectory in VMD -------- 1) Build a PSF file for use in viewing with VMD. This step works with VMD 1.9 and topotools 1.2. (Older versions, like VMD 1.8.6, don't support this.) a) Start VMD b) Menu Extensions->Tk Console c) Enter: (I assume that the the DATA file is called "system.data"  topo readlammpsdata system.data full animate write psf system.psf 2) Later, to Load a trajectory in VMD: Start VMD Select menu: File->New Molecule -Browse to select the PSF file you created above, and load it. (Don't close the window yet.) -Browse to select the trajectory file. If necessary, for "file type" select: "LAMMPS Trajectory" Load it. ---- A note on trajectory format: ----- If the trajectory is a DUMP file, then make sure the it contains the information you need for pbctools (see below. I've been using this command in my LAMMPS scripts to create the trajectories: dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz It's a good idea to use an atom_style which supports molecule-ID numbers so that you can assign a molecule-ID number to each atom. (I think this is needed to wrap atom coordinates without breaking molecules in half.) Of course, you don't have to save your trajectories in DUMP format, (other formats like DCD work fine) I just mention dump files because these are the files I'm familiar with. 3) ----- Wrap the coordinates to the unit cell (without cutting the molecules in half) a) Start VMD b) Load the trajectory in VMD (see above) c) Menu Extensions->Tk Console d) Try entering these commands: pbc wrap -compound res -all pbc box ----- Optional ---- Sometimes the solvent or membrane obscures the view of the solute. It can help to shift the location of the periodic boundary box To shift the box in the y direction (for example) do this: pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} pbc box -shiftcenterrel {0.0 0.15 0.0} Distances are measured in units of box-length fractions, not Angstroms. Alternately if you have a solute whose atoms are all of type 1, then you can also try this to center the box around it: pbc wrap -sel type=1 -all -centersel type=2 -center com 4) You should check if your periodic boundary conditions are too small. To do that: select Graphics->Representations menu option click on the "Periodic" tab, and click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. 5) Optional: If you like, change the atom types in the PSF file so that VMD recognizes the atom types, use something like: sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf (If you do this, it might effect step 2 above.) 以上为lammps mailing list某位大神的回帖关于vmd如何读入lammps trajectory，读入之后就可以制作动画了。 |
3楼2014-01-12 00:23:33
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4楼2014-01-14 17:14:18