![]() In this example, a single POPE molecule is displayed as lines. 3) Once a file is loaded, it will appear in the VMD Display window. A file is loaded by clicking the Load button. (The early stages of setting up a molecular dynamics simulation are never fun. Once a file is selected the Molecule File Browser will determine the file type. With the obtained data files of LAMMPS (and a little editing them) and ltemplify.py in the mentioned method in the link I got the solution/interface data file for a DPD simulation. Then using fix deform in LAMMPS I got the desired box size. To fix it, I made new xyz and data files again using Packmol and Moletemplate, respectively, but in a quite larger box (5 times larger). You were completely right, my data files had problems. Many thanks for looking at the files and your time!Īctually, I tried topo writelammpsdata, but it just made a data file of one of the opened data files.īut I again tried moletemplate, this time, with the new data files. (The early stages of setting up a molecular dynamics simulation are never fun.) This will prevent you from including bonds in your system. It seems like you are using “atom style atomic”. There is another problem: You should be using “atom_style molecular” (or preferably “atom_style full”). ![]() This now allows to do a large variety of modifications to topology data or even building topologies from. not only bonds, but also angle, dihedral, and improper definitions as well as their force field type labels (if available). It’s usually too tricky to try and do everything at once on the first try. Starting with VMD version 1.8.7 it is now possible to store the complete topology information, i.e. Once you have that working, then you can try combining them into one big system. Once it does, then try building the other system (the polymer system). ![]() Try to build that system correctly, and check it visually using VMD+topotools to confirm that it looks correct. Start with the simpler system (for example, the wall system). I suggest that you focus your efforts on building each system independently. Not much at this stage we can do to fix it. My guess would be that whatever went wrong occurred long ago, before you created the system1.data and system2.data files. It looks like the atoms in these two data files really are mixed together. (Incidentally, if you want to merge the two data files, you can follow this with a “writelammpsdata” command. I looked at the two data files using VMD+topotools by selecting the “Extensions”->“Tk Console” menu option and entering these commands: Incidentally, VMD+topotools can view multiple data files at the same time (without needing to merge them beforehand).
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