[gmx-users] g_polystat

Moeed lecielll at googlemail.com
Sat Sep 4 23:16:20 CEST 2010

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?

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?

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100904/9cac4d47/attachment.html>

More information about the gromacs.org_gmx-users mailing list