[gmx-users] trjcat set timestep/amb2gmx?

[francesco oteri]

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