On 9/03/2010 10:13 PM, pol...@fh.huji.ac.il wrote:
Dear Gromacs users and developers,
I'm trying to visualize .trr from md simulation using VMD.
I see that starting from some point (probable as a result of a peptide
drift ) my peptide splits and it seems like one part appears at one side
of the box and the other on the opposite side. Both parts are connected
with a very long bond. I want to center the peptide in the box and of
course I want all the molecules to be wrapped accordingly. I checked the
mailing list and I found that I can use trjconv (trjconv -f *.xtc -s
*.tpr -o center.xtc -center -pbc nojump). I tried to use this command
with .trr (trjconv -f *.trr -o center.trr -center -pbc) as a result the
peptide is still not centered and all the water molecules diffuse out of
my rectangular box. Am I doing something wrong? I'm trying to center the
molecule not only for visualization but also because I want to analyze
the simulation using VMD and scripts I made for analysis of NAMD
simulations (I worked with NAMD for a long time and I need to work with
gromacs because of SPCE water).
OK, well keep playing with the trjconv options and choosing sensible
groups for centering until you find something that pleases you. You may
need to do two different trjconv operations - one to center the peptide
and one to group the waters in the same periodic cell as the peptide.
Is it possible to perform analysis with
VMD (I need commands like measure distance, measure angle, cut molecules
at some radius from predefined residue and pbcwrap around some molecule
or peptide)?
Yup.
Mark
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