<div style="font-family: 'Times New Roman'; font-size: 16px;">Dear Justin,<br _moz_dirty="" /><br _moz_dirty="" />thank you for response and I am sorry not to define my problem properly. I have used the first alternative, which you discribed and thus obtained the weird resluts. Before I used this alternative I did what you mentioned as the second alternative if I understood it correctly. I have specified the first and the last atoms of each chain as separate groups. But this makes 64 pairs of groups for 64 chairs and I need to apply 64 times g_dist, please, could you correct me if I am wrong? If I am right than it is better to write a script. <br _moz_dirty="" /><br _moz_dirty="" />I am appending the example of my group definitions <br _moz_dirty="" /><br _moz_dirty="" />[ PEO1_&_CH3 ]<br _moz_dirty="" />1 87 173 259 345 431 517 603 689 775 861 947 1033 1119 1205<br _moz_dirty="" />1291 1377 1463 1549 1635 1721 1807 1893 1979 2065 2151 2237 2323 2409 2495<br _moz_dirty="" />2581 2667 2753 2839 2925 3011 3097 3183 3269 3355 3441 3527 3613 3699 3785<br _moz_dirty="" />3871 3957 4043 4129 4215 4301 4387 4473 4559 4645 4731 4817 4903 4989 5075<br _moz_dirty="" />5161 5247 5333 5419<br _moz_dirty="" />[ PEON_&_CH3 ]<br _moz_dirty="" />83 169 255 341 427 513 599 685 771 857 943 1029 1115 1201 1287<br _moz_dirty="" />1373 1459 1545 1631 1717 1803 1889 1975 2061 2147 2233 2319 2405 2491 2577<br _moz_dirty="" />2663 2749 2835 2921 3007 3093 3179 3265 3351 3437 3523 3609 3695 3781 3867<br _moz_dirty="" />3953 4039 4125 4211 4297 4383 4469 4555 4641 4727 4813 4899 4985 5071 5157<br _moz_dirty="" />5243 5329 5415 5501<br _moz_dirty="" /><br _moz_dirty="" />which provided weird results<br _moz_dirty="" /><br _moz_dirty="" />[ R1 ]<br _moz_dirty="" />1<br _moz_dirty="" /><br _moz_dirty="" />[ R11 ]<br _moz_dirty="" />83<br _moz_dirty="" /><br _moz_dirty="" />[ R2 ]<br _moz_dirty="" />
87<br _moz_dirty="" />
<br _moz_dirty="" />
[ R22]<br _moz_dirty="" />
169<br _moz_dirty="" /><br _moz_dirty="" />till [ R64 ] [ R6464 ] pairs which step-by step gave realistic results.<br _moz_dirty="" />
<br _moz_dirty="" />Thank you in advance<br _moz_dirty="" /><br _moz_dirty="" />Zuzana.<br /><br _moz_dirty="" /><br _moz_dirty="" /><br /><span>Dňa 02/18/10, <b class="name">"Justin A. Lemkul" </b> <jalemkul@vt.edu> napísal:</span><blockquote cite="mid:4B7D86E9.3010709@vt.edu" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text plain"><br /><br />Zuzana Benkova wrote:<br />>Dear GROMACS users,<br />><br />>I have a system of 64 chains and want to calculate averaged values of end-to-end distance of all chains as well as the averaged radius of gyration from 1ns trajectory. In the case of end-to-end distance I have prepared index file containing one group of the first atoms in ascending order and the second one containing the terminal atoms in ascending order. I have used g_dist but it looks like it combined all pairs between both groups. I have looked at the mailing list but did not find the answer.<br />><br /><br />g_dist should only be measuring the COM distance between the two selected groups, so I don't know what you mean by "combined all pairs" - perhaps you can provide an example (index groups, relevant output, what you were expecting, and why you think it's wrong)? If your groups contain all starting residues in one, then all ending residues in another, then yes, you're going to get weird results. If you have one chain that is residues 1-100, you should have a group for r_1 and a group for r_100; select those for g_dist analysis. If another chain is residue 101-200, r_101 and r_200 are what you want, etc.<br /><br />>Is it possible to do such analysis using directly GROMACS tools or I need to prepare some scripts with loops running over all chains. Thank you for response in advance.<br />><br /><br />It certainly should be possible to iteratively use g_dist to measure distances between whatever groups you select. Fairly straightforward, actually, so if you're not getting what you expect, provide the information I asked for above and hopefully someone should be able to figure out what's going wrong.<br /><br />-Justin<br /><br />>Zuzana Benkova<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 /><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br /><br />========================================<br />-- <br />gmx-users mailing list gmx-users@gromacs.org<br /><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br />Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br />Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request@gromacs.org.<br />Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br /></div></blockquote></div>