gmx3 at hotmail.com
Mon Sep 6 10:07:25 CEST 2010
> Date: Sat, 4 Sep 2010 17:50:46 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] g_polystat
> 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.
For the radius of gyration you can choose any group you like.
For the persistence length the programs compares directions of vectors between
consecutive atoms in the index group, so you usually want only atoms in the main chain
for that (no hydrogens etc).
As the manual says, the selected group is split into molecules, it will always analyze
every molecule separately and average the results.
> > 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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