[gmx-users] image jumps in VMD

[Richard Filmer]

On Tue, 25 Jun 2002, Dr. Y. U. Sasidhar wrote:

> Richard Filmer wrote:
> 
> >This will create a trjectory file with the proteins centered.
> >
> >trjconv -f input.trr -o output.trr -s input.gro -center -pbc whole
> >  
> >
> We tried your advice. It works with ngmx, but not with  VMD.
> For some reason VMD is seeing only one frame. Any further thoughts on this ?
> Sasidhar


if the atoms in your trr file do not match up exactly with your gro file,
VMD will only see one frame (ie. it will read the gro file). 

When running trjconv, first select 'protein' in choosing what to center,
then 'system' in choosing what to write to file. Make sure you have a gro
file that matches your trr (includes all water and ions, etc.). 




> 
> >  
> >
> >>I use vmd_1.72 to visualize gromacs md trajectory using "animate".
> >>1. Frequently the image jumps between edges and goes out of visible
> >>screen window.
> >>How do I avoid this ? ( centering in a frame also does not work ).
> >>How can I have image always in field of view so that I can view
> >>trajectory completely without "interruptions".
> >>
> >>2. Can I save pdb file of a particular frame number in VMD ?
> >>
> >>Sasidhar
> >>
> >>
> >>
> >>
> >>
> >>
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