[gmx-users] Water removed from system and visualizing protein alone in VMD. But problem in visualization of all frames (sun)

[Björn Sommer]

> 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
>
> Regards
> Suniba
Hi Suniba,

sorry, but this is not the way how you should use VMD! It is much more 
comfortable.

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 
selection.

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

resname SOL

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 
stlye" tab.

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.

Have fun!
Bjorn