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.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
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
--
========================================
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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