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

[Berk Hess]

I just realized that in 4.0 I modified things such that it only
prints the bonds per molecule type.
It would be quite easy to modify a program to write all bonds.
(mk_angdx for instance).

If you just have one atom type you can easily modify
your script by reading the number of molecules and atoms_mol
from the molblock print in the gmxdump output.

Berk

From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] List of all bonds form tpr file?
Date: Wed, 26 Nov 2008 11:52:45 +0100








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: yesint4 at yahoo.com
> To: gmx-users at 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 <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/
> 
> Mark
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