[gmx-users] regarding g_sas and rdf

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 9 20:26:36 CEST 2012

priya thiyagarajan wrote:
> hello sir,
> thanks for your kind reply...
> to study about micelle formation is it correct to use g_polystat. to 
> measure gyrate...

Probably not.  There are a variety of other tools that are probably more 
applicable.  Check the manual, Chapter 8 and Appendix D, along with the mailing 
list archive.  There have been a large number of discussions regarding micelles. 
  For the future, it would be far more effective for you to state your objective 
up front rather than after an initial attempt has been made to help.  That way, 
you'll avoid potentially misleading advice.  My assumption was that you had 20 
molecules for which you wished to obtain end-to-end distances and/or Rg values. 
  It sounds like you want some metrics related to micelle size, which is very 

> also i tried g_sas to find the solvent accessible surface and g_rdf..
> but i dono how to interpret the result from the graph..
> i gave calculation group and output group as protein.
> since i am using these commands newly i dono to interpret it ..
> please give me some brief description about how to interpret the result 
> from plot..
> i searched but i couldnt get it clearly..

No one's going to be able to help in this regard.  Simply stating you don't 
understand your output doesn't give anything to go on.  Read the citations 
provided by the screen output of g_sas regarding the underlying method.  Read 
g_sas -h for available options and what they do.  Then read the headers in the 
.xvg file to understand what the data sets are.  If you have something more 
specific that can be addressed, post back once you've done all this.

As for g_rdf, there is a nice discussion of what an RDF is and how it can be 
used in the manual, section 8.4.



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


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