[gmx-users] Water removed from system and visualizing protein alone in VMD. But problem in visualization of all frames (sun)
bjoern at CELLmicrocosmos.org
Thu Feb 4 23:30:24 CET 2016
> Hello Everyone
> I have performed a md simulation if protein in water for 10ns and frames were obtained after every 10ps. I wanted to visualize the.gro and trajectory file in VMD, without water, so I prepared an index file containing protein only. Using editcon i removed water from md.gro as well but I loaded the files in VMD, 1000 time frames are loaded but I cannot see any change in structure or per frame conformation. The protein is still. I am not clear what to do. I tried keeping water in .trr and then in .gro and repeated steps but no results. When I use original .trr and .gro, only then i visualize the change in structure. Please help me
sorry, but this is not the way how you should use VMD! It is much more
You first import the PDB file, then you import the TRR or XTC file (make
sure that the actual PDB file is selected during loading, so that the
trajectory is associated with it). You may also first make the following
settings after importing the PDB, and then afterwards import the
trajectory. This might save time during loading and memory resources.
Okay, you open now the representations window (Graphics -> Representations).
In the Representations window, select the tab "Selections". In the
keyword section, select "resname". Now, you will see in the field value
all Residue IDs contained in your PDB file. Use this IDs now in the
For example, water has often the name SOL or WAT etc. If you want to see
only the water, type in into the "Selected Atoms" section
If you want to see everything else, not the water, and also not the
ions, which could have the name NA, you say
not resname SOL NA
You want to see only the P atoms of DPPE with the resname DPE
(resname DPE) and (name P8')
Please note that, to select single molecules, you should have a look to
the original PDB file and check what the names of the atoms for the
corresponding molecule look like.
To change now the representations, you find all options in the "Draw
Now you want to have different representations for different atoms: just
click on "Create Rep". The last representation is duplicated, and you
can change it now. By double clicking on the entry in the list, you can
hidea an entry.
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