On 8/16/12 4:19 PM, tdgrant1 wrote:
No they do not. The trajectory contains all the atoms, including the solvent
(~300,000 atoms), whereas the structure passed to -s is the averaged
structure from the last 60ns of simulation and only includes the non-solvent
atoms (~15,000). Should I rerun rmsf on the last 60ns but select System
instead of non-solvent, and then use that averaged structure to pass to the
-s flag?
I don't see how getting the average structure of a 300k atom system is
meaningful - that will certainly chew up lots of memory ;)
What I would suggest is one of the following:
1. Create a .tpr file with your averaged structure from an existing topology and
run g_rmsf.
2. Use trjconv to create a subset trajectory (.xtc) that matches the number of
atoms in the reference structure.
3. Avoid ever choosing "System" for analysis - choose the backbone or whatever
custom index group you wish to use. I don't see an inherent problem with using
the "System" in the reference structure (your RNA) but you never know when
there's some curious mismatch in the interpretation down the line. Could be a
bug, but I'm not prepared to believe that yet from the evidence at hand.
-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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