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<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><blockquote><hr id="EC_stopSpelling">From: gmx3@hotmail.com<br>To: vvchaban@gmail.com<br>Subject: RE: [gmx-users] Dynamical atom groups in 'index.ndx'<br>Date: Wed, 25 Jun 2008 15:31:59 +0200<br><br>
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<div style="text-align: left;">Hi,<br><br>I think this would require complete rewriting of all the (required) analysis tools.<br>Currently all tools assume that you have a static, fixed length list of atoms.<br>You can not "simply" make this list dynamic.<br>It would be very useful to have such a functionality, but one would like to<br>have this implemented at a higher level.<br></div><br>There is currently a (limited) similar functionality via trjorder.<br>trjorder can order atoms based on distance. This effectively makes<br>you index group dynamic, but the size is fixed.<br>(although not for g_velacc, which needs time correlation, but there<br>it becomes difficult to define what you want to calculate exactly<br>with dynamic groups)<br><br>Berk.<br><br><br><hr id="EC_stopSpelling">> Date: Wed, 25 Jun 2008 15:35:46 +0300<br>> To: gmx-users@gromacs.org<br>> From: vvchaban@gmail.com<br>> Subject: [gmx-users] Dynamical atom groups in 'index.ndx'<br>> <br>> Dear Colleagues,<br>> <br>> Did not anybody try to implement a possibility to use a changeable<br>> 'index.ndx' when analyzing a trajectory (g_rdf, g_velacc, etc)?<br>> I mean that the atoms numbers in 'index.ndx' could change,<br>> being different for different frames.<br>> <br>> This trick can be used for evaluating properties of molecules located<br>> in the definite area at the current moment. Now we can control the<br>> particles but how can we check if these particles are still located<br>> in the same area where they were before they started to move?<br>> <br>> Of course, one is able to do it by visualizing trajectory and then<br>> edit the particles number by hand but it is quite unlucky solution, as<br>> for me.<br>> <br>> Probably I'll try to make something like it if time permits.<br>> If somebody has got any considerations on this topic, please let me know.<br>> <br>> -- <br>> Vitaly V. Chaban<br>> School of Chemistry<br>> National University of Kharkiv<br>> Svobody sq.,4, Kharkiv 61077, Ukraine<br>> email: chaban@univer.kharkov.ua<br>> skype: vvchaban<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.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><br><hr>Express yourself instantly with MSN Messenger! <a href="http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/" target="_blank">MSN Messenger</a>
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