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<br><br>> Date: Sat, 4 Sep 2010 17:50:46 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] g_polystat<br>> <br>> <br>> <br>> Moeed wrote:<br>> > Hello Justin,<br>> > <br>> > I have read help of the command I am using several times. My <br>> > understanding is that g_polystat calculates Rg of 8 chains and takes the <br>> > average if no specific index groups are selected. Below are the groups I <br>> > have created for 8 chains.<br>> > g_polystat -f *.trr -s *.tpr -o polystat-mw-xvgr-8group -n *.ndx -mw <br>> > -xvgr -w -p persist.xvg<br>> > then chose 0 1 2 3 4 5 6 7 as se;ected groups. The point is Rg for this <br>> > 8 molecules is similar to that When I select group 0 only. If Rg is the <br>> > average of all chians over time why is it giving Rg of first chain?<br>> > <br>> <br>> g_polystat does not accept multiple input groups, so if you're entering "0 1 2 <br>> 3..." at the index prompt, then only group 0 is selected. The tool will print <br>> which group it is analyzing. I think this is generally true for all Gromacs <br>> tools. Try analyzing a group that contains all your polymers.<br>> <br>> > Also as for persistence lenght -h option says:<br>> > The chosen index group<br>> > should consist of atoms that are consecutively bonded in the polymer<br>> > mainchains. My groups start from atom 1 to 8*362 consecutively... Do you <br>> > any clue why I am mot getting output file?<br>> > <br>> <br>> Not really. But if you're including all atoms in the analysis, then you're not <br>> analyzing main chain atoms, as the tool expects. Try creating an index group of <br>> only one molecule, and only its main chain (presumably non-H) atoms. From the <br>> description, it also sounds like the group selected should contain "atoms that <br>> are consecutively bonded." Whether or not that excludes the possibility of <br>> analyzing multiple molecules at once, I don't know, but atoms that are not <br>> consecutively bonded should not be included in the analysis.<br><br>For the radius of gyration you can choose any group you like.<br>For the persistence length the programs compares directions of vectors between<br>consecutive atoms in the index group, so you usually want only atoms in the main chain<br>for that (no hydrogens etc).<br><br>As the manual says, the selected group is split into molecules, it will always analyze<br>every molecule separately and average the results.<br><br>Berk <br><br>> <br>> -Justin<br>> <br>> > <br>> > Group 0 ( PE60-1) has 362 elements<br>> > Group 1 ( PE60-2) has 362 elements<br>> > Group 2 ( PE60-3) has 362 elements<br>> > Group 3 ( PE60-4) has 362 elements<br>> > Group 4 ( PE60-5) has 362 elements<br>> > Group 5 ( PE60-6) has 362 elements<br>> > Group 6 ( PE60-7) has 362 elements<br>> > Group 7 ( PE60-8) has 362 elements<br>> > <br>> > Thank you<br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>                                            </body>
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