README_visualize.txt
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README_visualize.txt
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			NOTE: VMD DOES NOT ALLOW YOU TO VISUALIZE SYSTEMS WITH MANY BONDS ATTACHED
			TO EACH ATOM. (IF IT DID, THE RESULTS WOULD BE UGLY ANWAY.)

			HOWEVER THIS MODEL ATTACHES APPROXIMATELY 60 BONDS TO EACH CONDENSIN ATOM.
			IN ORDER TO PULL THE CONDENSIN MONOMERS TOGETHER. YOU MUST DELETE THOSE
			BONDS (of type "1" or "2") FROM THE "system.data" FILE BEFORE YOU CARRY
			OUT THE COMMANDS BELOW. (...And backup your "system.data" file. You'll need
			all the bonds when you run the simulations.)

			-------------- COLORS ---------------
			In order to show how the polymer is distributed along the length of the
			cylinder, I recommend to select the
			Graphics->Graphical Representations
			menu option, and select "Index" from the "Coloring Method" pull-down menu.

			After doing this, you can switch from a red-white-blue scheme, to a
			rainbow ("jet") scheme, by selecting the Extensions->Tk Console menu option
			and loading the "vmd_colorscale_jet.tcl" file located in the "images" directory.
			-------------------------------------------

			First, if you have not done so, download and install VMD:

			http://www.ks.uiuc.edu/Research/vmd/
			http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD


			------- To view a lammps trajectory in VMD --------

			The system coordinates are initialy stored in a LAMMPS' ".data" file.
			(If that file was built with moltemplate, it will be named "system.data".)

			The first step is to view that file.
			Then you should create a ".psf" file
			(The .psf file is necessary after you run the simulation
			for viewing trajectories.)

			1) Build a PSF file for use in viewing with VMD

			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

			You will see a snapshot of the system on the screen.
			(presumably the initial conformation at t=0)

			2)

			Later once you have run a simulation,
			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
			(It usually has names like "traj.lammpstrj". It depends on how you saved it.)
			If necessary, for "file type" select: "LAMMPS Trajectory".
			(However VMD should recognize the file type by the file extension.)
			Load it.





			##################### PERIODIC BOUNDARY CONDITIONS #####################
			If you are only simulating a single molecule and you are not
			using periodic boundary conditions, then ignore everything below.
			########################################################################

			---- A note on trajectory format: -----
			If the trajectory is the standard LAMMPS format, (aka a "DUMP" file with
			a ".lammpstrj" extension), then it's a good idea when you run the simulation
			to tell LAMMPS you want to store the information needed for showing periodic
			boundary conditions. (Even if you are not using periodic boundaries.
			It never hurts to include a tiny bit of extra information.) To do that,
			I've been using this command in my LAMMPS scripts to create the trajectories:

			dump 1 all custom 5000 traj.lammpstrj id mol type x y z ix iy iz

			(Also: 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 visually without breaking molecules in half. Again
			you don't need to worry about this if you are not using periodic boundaries.)


			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 {-0.5 -0.5 -0.5}
			pbc box -shiftcenterrel {-0.5 -0.5 -0.5}

			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.)

lammps/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/README_visualize.txt12150ffa7397lammm-devel

README_visualize.txtView Options

lammps/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/README_visualize.txt
12150ffa7397lammm-devel

README_visualize.txt
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