[gmx-users] center peptide in simulation box

politr at fh.huji.ac.il politr at fh.huji.ac.il
Tue Mar 9 12:13:33 CET 2010

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). 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)?

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