[gmx-users] Re: RMSF error when fitting to average structure

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


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