[gmx-users] Re: Actual box size

Justin Lemkul jalemkul at vt.edu
Tue Dec 18 20:06:37 CET 2012

On 12/18/12 2:04 PM, zugunder wrote:
> Justin Lemkul wrote
>> If you don't specify an actual file name to -s, then all Gromacs tools
>> look for a default file name, which in this case is "topol.tpr."  Since
>> you've run a simulation, clearly you have a .tpr file, which is what you
>> need to provide to -s.
> I have only one .tpr file - the input for NVT (which I'd like to convert).
> Is it the one? However, when I execute:
> g_trjconv -f nvt_minimized.cpt -o nvt_minimized_compact.xtc -s
> nvt_min_input.tpr -pbc mol -ur compact
> I have a very small file (~100k) as an output and VMD reports only one frame
> in it (no image).

Because VMD can't deal with an .xtc file with no reference coordinate file.  If 
you want a coordinate file, specify a coordinate file (not trajectory) to the -o 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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