----- Original Message ----- From: Hassan Shallal <hshal...@pacific.edu> Date: Saturday, June 5, 2010 13:52 Subject: [gmx-users] visualizing small molecule in a trajectory file .trr and .gro using VMD To: gmx-users@gromacs.org Cc: vm...@mailhost.ks.uiuc.edu
----------------------------------------------------------- | > 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? Not without understanding how selections work in VMD, which must be in their documentation (hint, hint). Probably you want to select "resname UNK" - but be sure you've done the VMD tutorials because I'm sure they illustrate this idea. > 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... VMD can do it, you just need to learn how to instruct it :-) Mark | -----------------------------------------------------------
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