[gmx-users] How to add connectivity information in the trajectory file?

[Liao Chuan]

Dear all,

Is it possible to add connectivity information in the trajectory file?  I'm
dealing with CG MD using Martini FF.  After the production run, I checked my
trajectory by loading the full.gro and full.trr in VMD. However, I could see
nothing but a stack of CG beads moving around. No bonds there.  

It was mentioned that (maybe in the revision history, I couldn't find it any
more as gromacs is moving to a new site) Gromacs 4.0.5 is able to add
connectivity information in the trajectory file, which is very helpful in CG
simulation. I got one trajectory file in pdb format  by trying the following
command:

Trjconv -f full.trr -s full.tpr -n index.ndx -o test.pdb

I checked the test.pdb(with many frames) and found no connectivity
information. How could I add connectivity information in the trajectory
file? 

Any suggestions are greatly appreciated!

Many thanks in advance!!

 

 

Yours, 

Chuan Liao

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