[gmx-users] Re: RMSF error when fitting to average structure
jalemkul at vt.edu
Thu Aug 16 22:49:40 CEST 2012
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
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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