[gmx-users] trjcat set timestep/amb2gmx?

[Steven Neumann]

What do you mean by style 8?


On Tue, Apr 16, 2013 at 4:51 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> See style 8 for trjconv -h
>
> Mark
>
>
> On Tue, Apr 16, 2013 at 10:26 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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