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

[Mark Abraham]

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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