[gmx-users] Martini force field: elastic network

XAvier Periole x.periole at rug.nl
Fri Oct 14 18:17:33 CEST 2011

The website has been updated to fit a CG tutorial  starting monday in  
The manner of the construction you describe in your email is not the  
proper way to do it!

The new script is doing it properly.

If you want the old script to only generate the elastic network (as it  
seems from your email) you may have it or use the scripts from the  
ElNeDyn approach.


On Oct 14, 2011, at 5:58 PM, Li, Hualin wrote:

> Dear all,
>          I am using martini force field to generate elastic network  
> for my protein. I generate a list of distance between all beads  
> within a certain distance by:
>     genrestr -f  ***.gro -n index.ndx -constr -o constraints
>        getting the constraints.itp file and will continue with the  
> 2nd step by using a script:
>    ./select_restr.pl constraints.itp 0.5 0.9 500
>       However, the martini forcefield developer seems to update  
> their website yesterday and I can't find the select_restr.pl any  
> more and in the new script they provide ( martinize.py),  -elastic    
> to write elastic bonds is not working yet.  Could some one provide  
> me the old script   "select_restr.pl" please?
>      Many thanks.
> ---hualin--
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