[gmx-users] trjcat set timestep/amb2gmx?

[Steven Neumann]

Thank you all.

Would you suggest any link to a script like amb2gmx.pl ? I cannot fina
anything like this - basically I wish to convert top.prmtop to top.tpr.




On Tue, Apr 16, 2013 at 9:26 AM, francesco oteri
<francesco.oteri at gmail.com>wrote:

> Hi,
> yes Marc you are right but the last time I used gromacs on a namd
> trajectory
> I noticed that time in the output files is useless 'cause it is always 0.
> I understand that, since this information is usually took from .trr or
> .xtc, it cannot
> be extracted from a .dcd, but it could be more useful using as x the frame
> number.
> This could, at least, permitting to visualize the plot with xmgrace without
> postprocessing
> the .xvg
>
>
>
> Francesco
>
>
> 2013/4/16 Mark Abraham <mark.j.abraham at gmail.com>
>
> > On Apr 15, 2013 6:27 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
> > >
> > >
> > >
> > > On 4/15/13 12:23 PM, Steven Neumann wrote:
> > >>
> > >> Dear Gmx Users,
> > >>
> > >> I obtained dcd trajectory from simulation in another software. I wish
> to
> > >> merge many trajectories using trjcat with a proper timestep. Is that
> > option
> > >> possible using gromacs or shall use a script to produce tpr file from
> my
> > >> prmtop file e.g. amb2gmx ? Any links for such a script?
> > >>
> > >
> > > If you linked against VMD libraries when installing, Gromacs can handle
> > any trajectory/coordinate file format that VMD can, thus requiring no
> > conversion. If you need a .tpr file to do the analysis you are trying to
> > do, then yes, you need to convert topology information into the proper
> > format.
> >
> > ...and be aware that a -s option that accepts both .tpr and (say) .gro
> > formats (as shown in g_tool -h) might succeed with the latter if only
> atom
> > names, rather than (say)  bonding connectivity is required for g_tool to
> > work.
> >
> > Mark
> > > -Justin
> > >
> > > --
> > > ========================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Research Scientist
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540) 231-9080
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >
> > > ========================================
> > >
> > > --
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>
> --
> Cordiali saluti, Dr.Oteri Francesco
> --
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