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Hi,<br><br>Everything depends on what you want to accomplish, which you<br>do not write.<br>I don't see why you would want to look at single atoms.<br>Since you pull on COM's, only the COM coordinates are relevant.<br>If you want to look at single atoms, simply store them in the xtc file.<br><br>If you have only two groups, there is no physical difference between<br>the reference group and the first pull group. They are simply two<br>groups between which the distance is calculated and the forces act.<br>If you used an absolute reference, 0Z is the absolute reference coordinate,<br>not the coordinate of a group.<br><br>Berk<br><br>> Date: Tue, 23 Jun 2009 14:39:48 +0200<br>> From: ilona.baldus@bioquant.uni-heidelberg.de<br>> To: gmx-users@gromacs.org<br>> Subject: RE: [gmx-users] pullx.xvg Meaning of output?<br>> <br>> <br>> Dear Berk,<br>> <br>> Thanks for the quick reply. That leads me to my next questions:<br>> *I used the whole N and C residues for pulling. Is there any way of <br>> reconstructing the values for the single atoms? Or do you recommend <br>> only to pull N and C in the first place?<br>> *What does the reference group actually do? Can I simply leave it out? <br>> Does it influence pulling? What would be a good reference group? A <br>> random backbone atom from the middle of the protein?<br>> <br>> I'm looking forward to your reply. Thank you very much in advance.<br>> <br>> Best wishes, Ilona<br>> <br>> <br>> Quoting Berk Hess <gmx3@hotmail.com>:<br>> <br>> ><br>> > Hi,<br>> ><br>> > This is actually not (yet) documented.<br>> > 0Z is the Z-coordinate of group 0.<br>> > 1dZ is the the Z-coordinate of group 1 minus the one of group 0.<br>> ><br>> > Berk<br>> ><br>> >> Date: Tue, 23 Jun 2009 12:54:37 +0200<br>> >> From: ilona.baldus@bioquant.uni-heidelberg.de<br>> >> To: gmx-users@gromacs.org<br>> >> Subject: [gmx-users] pullx.xvg Meaning of output?<br>> >><br>> >> Hi!<br>> >><br>> >> I am trying to understand the output of my pulling simulation:<br>> >> I get a pullx.xvg file which shows 0Z, 1dZ, 2dZ after pulling in Z and<br>> >> -Z direction. I really cannot figure out the meaning of 1dZ and 2dZ.<br>> >> Since the website is down I cannot check on previous issues, so sorry<br>> >> for asking the same question again as I already asked last week but<br>> >> which remained unanswered.<br>> >><br>> >> I would appreciate any advice.<br>> >><br>> >> Thanks a lot. Ilona<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>> ><br>> > _________________________________________________________________<br>> > Express yourself instantly with MSN Messenger! Download today it's FREE!<br>> > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/<br>> <br>> <br>> <br>> Ilona Baldus<br>> MPI Stuttgart<br>> INF 276<br>> 69120 Heidelberg<br>> Tel.: 06221-5451268<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><br /><hr />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
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