Hi,
gmxdump in 4.0 still dumps all bonds.
I don't know what causes you not to see them.
Berk
> Date: Wed, 26 Nov 2008 02:09:08 -0800
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] List of all bonds form tpr file?
>
> 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!
>
> Semen
>
>
>
>
> ----- Original Message ----
> From: Mark Abraham <[EMAIL PROTECTED]>
> To: Discussion list for GROMACS users <gmx-users@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/
>
> Mark
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>
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