[gmx-users] How to add connectivity information in the trajectory file?
liaochuan at tju.edu.cn
Tue Jun 16 15:54:09 CEST 2009
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
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
Any suggestions are greatly appreciated!
Many thanks in advance!!
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