[gmx-users] g_polystat

Justin A. Lemkul jalemkul at vt.edu
Sat Sep 4 23:50:46 CEST 2010

Moeed wrote:
> Hello Justin,
> I have read help of the command I am using several times. My 
> understanding is that g_polystat calculates Rg of 8 chains and takes the 
> average if no specific index groups are selected. Below are the groups I 
> have created for 8 chains.
> g_polystat -f *.trr -s *.tpr -o polystat-mw-xvgr-8group -n *.ndx -mw 
> -xvgr -w -p persist.xvg
> then chose 0 1 2 3 4 5 6 7 as se;ected groups. The point is Rg for this 
> 8 molecules is similar to that When I select group 0 only. If Rg is the 
> average of all chians over time  why is it giving Rg of first chain?

g_polystat does not accept multiple input groups, so if you're entering "0 1 2 
3..." at the index prompt, then only group 0 is selected.  The tool will print 
which group it is analyzing.  I think this is generally true for all Gromacs 
tools.  Try analyzing a group that contains all your polymers.

> Also as for persistence lenght -h option says:
> The chosen index group
> should consist of atoms that are consecutively bonded in the polymer
> mainchains. My groups start from atom 1 to 8*362 consecutively... Do you 
> any clue why I am mot getting output file?

Not really.  But if you're including all atoms in the analysis, then you're not 
analyzing main chain atoms, as the tool expects.  Try creating an index group of 
only one molecule, and only its main chain (presumably non-H) atoms.  From the 
description, it also sounds like the group selected should contain "atoms that 
are consecutively bonded."  Whether or not that excludes the possibility of 
analyzing multiple molecules at once, I don't know, but atoms that are not 
consecutively bonded should not be included in the analysis.


> Group     0 (      PE60-1) has   362 elements
> Group     1 (      PE60-2) has   362 elements
> Group     2 (      PE60-3) has   362 elements
> Group     3 (      PE60-4) has   362 elements
> Group     4 (      PE60-5) has   362 elements
> Group     5 (      PE60-6) has   362 elements
> Group     6 (      PE60-7) has   362 elements
> Group     7 (      PE60-8) has   362 elements
> Thank you


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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