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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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