Liao Chuan wrote:
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.
Sure, this is expected. VMD uses heuristics to guess where bonds might
exist, and CG structures violate these. Read the VMD docs to work out
how to teach it new heuristics. You're probably not the first to have
this problem - search the VMD mailing list.
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?
It's news to me if you can add connectivity information. I don't see any
sign of it in the release notes
http://oldwww.gromacs.org/content/view/181/132/
You still don't need the connectivity information in the trajectory
file. A single PDB file with CONECT entries probably would suffice
(assuming VMD reads them), and then you import the trajectory in the
usual VMD manner.
Mark
Any suggestions are greatly appreciated!
Many thanks in advance!!
Yours,
Chuan Liao
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