[gmx-users] Extracting the last frame of simulation into PDB

Justin Lemkul jalemkul at vt.edu
Fri Feb 15 20:51:05 CET 2013

On 2/15/13 2:08 PM, zugunder wrote:
> Hi,
> I bumped into a small problem, I think I missed something... so I am asking
> for help.
> I made a simulation of a protein in water (35ns, extended 3 times from
> initial 10ns) and now I need to get a resulting protein structure in pdb.
> So I issued:
> g_trjconv -s md_input_extended_to35ns.tpr -f md_product.xtc -o
> md_product_35ns.pdb -dump 34999
> But the resulting pdb looks weird when I open it in VMD or Chimera - it
> looks like the structure is split into 2 parts (within one file) and I can
> see several huge gaps in coordinates when viewing the file content. Gromacs
> trjconv manual doesn't seem to describe this behaviour, so could I ask
> anyone to help me with this?

Molecules "breaking" is a normal consequence of periodicity and gets discussed 
pretty much daily on this list.


If you're interested in just the last snapshot, mdrun writes that out, so you 
don't necessarily need to process the whole trajectory to obtain it, just use 
editconf to produce whichever file format you like (though trjconv may be 
necessary to deal with periodicity, anyway).



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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