[gmx-users] trjcat set timestep/amb2gmx?

Mark Abraham mark.j.abraham at gmail.com
Tue Apr 16 01:06:31 CEST 2013

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
>> 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

...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

> -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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