I've since found the source of my problem - the program was measuring the (marginally shorter) distance across the PBC boundary, rather than the distance within the box. Unfortunately there doesn't seem to be a way to turn PBC images off (correct me if I'm wrong?), so I guess I'm going to do some jiggerypokery with the data and some math.
----- Original Message ---- > I've been using g_dist to plot distances along the normal to my bilayer > between groups. Namely in this case, between the phosphates of opposing > leaflets, and the peptide. I would expect the sum of the distances > between the peptide and each leaflet's phosphates to equal the distance > between the two sets of phosphates. But they mysteriously don't. I'm > taking the z-distance to be the final value in each row, as the headers > in the .xvg indicate: > > @ s0 legend "|d|" > @ s1 legend "d\sx\N" > @ s2 legend "d\sy\N" > @ s3 legend "d\sz\N" > 0.0000000 3.2837145 0.0671294 -0.0351439 -3.2828403 > > The index groups are definitely correct (doublechecked by using trjconv > -n -dump and visualising the groups so selected), so there's no error > there, I'm sure. And these are the numbers I get out for the first frame: > Peptide - leaflet 1 phosphates: -3.3361144 > Peptide - leaflet 2 phosphates: 0.2953452 > Leaflet 1 - leaflet 2 phosphates: -3.2828403 > Is there an error in my understanding of how this is working? I'm pretty > certain the first two numbers should sum to the value of the third > number. Alternatively, any idea what could be going wrong? The files > being used are definitely the same, too... > > Alan. > > > > _________________________________________________________________________ > ___________ Be a better friend, newshound, and > know-it-all with Yahoo! Mobile. Try it now. > http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
