[gmx-users] List of all bonds form tpr file?

Semen Esilevsky yesint4 at yahoo.com
Wed Nov 26 11:09:08 CET 2008

Dear All,
We have a script, which visualizes the bonds in the coarse-grained system simulated in gromacs. In gromacs 3.x it was reading dumps of the tpr files and extracted BONDS records. Now in 4.x it does not work because gmxdump no longer outputs all bonds in the system. Is it possible to extract information about *all* bonds in the system (not only the bonds in each moleculetype) from tpr file in 4.x?

Any help is appreciated!


----- Original Message ----
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wednesday, November 19, 2008 1:57:19 PM
Subject: Re: [gmx-users] Pulling in 4.0  - Any documentation?

Semen Esilevsky wrote:
> Dear All,
> Where can I find documentation about the pull code in Gromacs 4.0? As far as I understand old style of setting up pulling simulations in separate file does not work any more, but I can't figure out how to transfer pulling params correctly to mdp file. Any help is appreciated!
> P.S. Probably the developers could put at least some very brief docs on web site while new manual is being prepared? Otherwise new cool features of 4.0 just can't be used by ordinary users...

The beta manual is at ftp://ftp.gromacs.org/pub/beta/

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