VMD-L Mailing List

From: Collins Nganou (nganoucollins_at_gmail.com)
Date: Thu Aug 22 2013 - 08:05:12 CDT

Hi,

You can perhaps use the following way to convert your file in pdb file
trjconv -s x.tpr -f x.xtc -o traj.pdb -pbc nojump

then load the pdb file into vmd. It will work.....

You may also load your x.gro file and play with graphical representation
to select what you are looking for.

Best regards

Collins

On Wed, Aug 21, 2013 at 9:18 PM, Holden Ranz <htranz_at_ucdavis.edu> wrote:

> Hello,
>
> I am new to VMD and have installed vmd 1.8.7 OpenGL on my windows 7 32-bit
> OS (tried using 1.9.1, but Nvidia driver is 189 series so not suitable).
> PDB and LAMMPS trajectory files load fine, but when I go to load a .xtc
> file the screen appears blank.
>
> I get the following output when trying to load the file:
>
> Info) VMD for WIN32, version 1.8.7 (August 1, 2009)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 4 CPUs detected.
> Info) Free system memory: 928MB (45%)
> Info) OpenGL renderer: GeForce 310M/PCI/SSE2
> Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
> Info) Spaceball driver not installed. Spaceball interface disabled.
> Info) No joysticks found. Joystick interface disabled.
> Found 68 plugins or data handlers in directory
> 'C:/Program Files/University of
> Illinois/VMD/plugins/WIN32/molfile'.
> vmd > Info) Using plugin xtc for coordinates from file
> C:/Users/Holden/Documents
> /Computing/Martini/lipid-tutorial/bilayer-analysis/dspc/traj.xtc
> Info) Finished with coordinate file
> C:/Users/Holden/Documents/Computing/Martini/
> lipid-tutorial/bilayer-analysis/dspc/traj.xtc.
>
> The file is from a gromacs coarse-grained simulation of dspc lipid
> bilayer. Can you guys please help me figure out what might be the problem?
> Thanks so much!
>
> Holden
>
> --
> Holden T. Ranz
> Graduate Student
> Department of Chemical Engineering & Materials Science
> University of California, Davis
> htranz_at_ucdavis.edu
>