[gmx-users] Visualizing the system
Peter C. Lai
pcl at uab.edu
Sat Sep 22 08:27:01 CEST 2012
This is a VMD question, but try using manual selections, like:
"not resname POPC and not resname SOL and not resname NA and not resname CL"
as a selection that doesn't show popc, water, and ions, for example.
I haven't had issues with VMD confusing what a protein is or not, so maybe
there is a residue ordering issue or something going on with the gro file?
On 2012-09-21 11:19:51PM -0700, Shima Arasteh wrote:
> In order to see a system of protein and lipids, I use VMD. I called system.gro something similar to what is produced in KALP15 in DPPC. When I load system.gro and select protein, one of lipids is loaded with it.
> I am wondering if it is a problem with my system.gro? Or something with the applied visualization tool?
> Thanks in advance.
> gmx-users mailing list gmx-users at gromacs.org
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
More information about the gromacs.org_gmx-users