GROMACS version: 2021.4
GROMACS modification: Yes/No
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I am simulating a POPC bilayer membrane with water and ions.
I loaded my nvt.gro structure and loaded its nvt.trr trajectory file using vmd. This resulted in a messy senseless visualization resulting in just lines moving around. Same for npt files too. Can anyone help me out with this please? I saw a similar thread but am unable to figure out the problem with my case in particular. Attached is a drive link of the image:
I just found out that while in line and one/two other representations I get these weird lines, certain representations like dynamical bonds, licorice, vdw etc give me correct visualisation. As a confirmation, I ran the files for the lysozyme tutorial and again saw a similar trend wherein the lines representation messes things up but other representations don’t. And for the tutorial, I have followed exact steps without changing PBC specifications. So is it that certain representation types in VMD don’t inherently work that good for gromac trajectory visualization? Or is it that I need to ne extra careful with my PBC conditions to visualize my system even in line or other such sensitive to perturbation representations?
Yes, this is usually a problem in visualization. You can fix it by “unwrapping” the trajectory, that is post processing the trajectory to correct for bonds that are broken across PBC walls. The easiest way - in GROMACS - to fix this is to use trjconv tool.
By the way, this is also done in step 9 of the lysozime tutorial, specifically within this line
If you visualize in VMD md_0_1.xtc and md_0_1_noPBC.xtc you will see the difference. Unwrapping is important for visualization purposes but sometimes also for analysis, although this largely depends on whether the tools you are using are PBC sensitive or not (for example, in the tutorial the unwrapping is important because the RMSD can suffer from artifacts due to the protein crossing the PBC boundaries).