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

Sun Iba sun.iba2 at gmail.com
Fri Feb 5 05:35:24 CET 2016

Thank You very much :)


On Fri, Feb 5, 2016 at 4:00 AM, Björn Sommer <bjoern at cellmicrocosmos.org>

> 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
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