[gmx-users] visualizing small molecule in a trajectory file .trr and .gro using VMD

Hassan Shallal hshallal at PACIFIC.EDU
Sat Jun 5 05:49:33 CEST 2010

Dear Gromacs and VMD users.
I am trying to visualize a simulation in which a small molecule is interactiong with a protein in a water box. The simulation has been produced using gromacs. I am using VMD for that purpose. I use the .gro and the .xtc files to load the trajectory to the VMD. 
What's the problem then?
The problem is that I can't visualize anything in presence of water, so I need to have only the protein and the small moecule which is named UNK in the gro file, when I use selected atoms in the graphical representations in VMD to show the small molecule and I type UNK in the selected atoms, I get the following error message: 
the atom selection you typed couldn't be understood
Does that mean that I will never be able to visualize the small molecule? 
Either the protein alone or the whole solvated system can be visualized, but I can't visualize both the protein along with the small molecule without the water...Could that be because in the .mdp file, I have haad protein and nonprotein descriptions? and that's why VMD can't isolate the UNK from the water? I don't know...
Hey Justin, thanks alot for the prompt help with the other question I have had about snapshots...
Any hint would be very appreciated...
Thanks alot
Hassan Shallal
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