RE: [gmx-users] g_mindist -or inconsistencies with atom-pairs
Thank you very much Ran, Will do. -Shay -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Ran Friedman Sent: Tuesday, December 22, 2009 16:53 To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_mindist -or inconsistencies with atom-pairs Dear Shay, What do you get when -or is present? Do the atoms always belong to the same residues? I suspect that since the calculation of the minimal distance is made for all residues, what you get at the end is the atoms at minimal distance between the last two residues. This seems like a bug and I suggest you submit a bugzilla. As a side note I think that the output will be given only for the last two groups in case there are more than two. You may want to check this as well if you submit a bug report. It should be too difficult to fix, but would involve changes in a few places in the code. Best regards, Ran. shaya...@post.tau.ac.il wrote: Dear Gromacs users, We used g_mindist analysis as follows: g_mindist -f *.xtc -s *.tpr -o atom-pairs.out -od mindist.xvg -or res_mindist.xvg and surprisingly in the atom-pairs.out only several atoms in one residue (from group 1) were at minimum distance from group 2 throughout the entire simulation. Checking this output manually showed it to be incorrect. res_mindist.xvg seems to hold the correct data. When running the same analysis, only omitting the -or flag, we get a *correct* atom-pairs.out. g_mindist -f *.xtc -s *.tpr -o atom-pairs.out -od mindist.xvg Comparing mindist.xvg from both scenarios shows no difference (files are identical). Is the -or flag supposed to affect the other output files of the g_mindist function? Supplementary details: 1. The same thing happened when g_mindist -s was supplied with either .gro, .pdb or .tpr files. 2. Index-groups 1 and 2 consisted upon full molecules with no ommisions (full protein and not only C-alpha). 3. We ruled out PBC by using -nopi 4. This is common with the following Gromacs versions: 3.3.3., 4.0.5, 4.0.7. Regards, -Shay --gmx-users mailing listgmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_mindist -or inconsistencies with atom-pairs
Dear Gromacs users, We used g_mindist analysis as follows: g_mindist -f *.xtc -s *.tpr -o atom-pairs.out -od mindist.xvg -or res_mindist.xvg and surprisingly in the atom-pairs.out only several atoms in one residue (from group 1) were at minimum distance from group 2 throughout the entire simulation. Checking this output manually showed it to be incorrect. res_mindist.xvg seems to hold the correct data. When running the same analysis, only omitting the -or flag, we get a *correct* atom-pairs.out. g_mindist -f *.xtc -s *.tpr -o atom-pairs.out -od mindist.xvg Comparing mindist.xvg from both scenarios shows no difference (files are identical). Is the -or flag supposed to affect the other output files of the g_mindist function? Supplementary details: 1. The same thing happened when g_mindist -s was supplied with either .gro, .pdb or .tpr files. 2. Index-groups 1 and 2 consisted upon full molecules with no ommisions (full protein and not only C-alpha). 3. We ruled out PBC by using -nopi 4. This is common with the following Gromacs versions: 3.3.3., 4.0.5, 4.0.7. Regards, -Shay -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_mindist -or inconsistencies with atom-pairs
Dear Shay, What do you get when -or is present? Do the atoms always belong to the same residues? I suspect that since the calculation of the minimal distance is made for all residues, what you get at the end is the atoms at minimal distance between the last two residues. This seems like a bug and I suggest you submit a bugzilla. As a side note I think that the output will be given only for the last two groups in case there are more than two. You may want to check this as well if you submit a bug report. It should be too difficult to fix, but would involve changes in a few places in the code. Best regards, Ran. shaya...@post.tau.ac.il wrote: Dear Gromacs users, We used g_mindist analysis as follows: g_mindist -f *.xtc -s *.tpr -o atom-pairs.out -od mindist.xvg -or res_mindist.xvg and surprisingly in the atom-pairs.out only several atoms in one residue (from group 1) were at minimum distance from group 2 throughout the entire simulation. Checking this output manually showed it to be incorrect. res_mindist.xvg seems to hold the correct data. When running the same analysis, only omitting the -or flag, we get a *correct* atom-pairs.out. g_mindist -f *.xtc -s *.tpr -o atom-pairs.out -od mindist.xvg Comparing mindist.xvg from both scenarios shows no difference (files are identical). Is the -or flag supposed to affect the other output files of the g_mindist function? Supplementary details: 1. The same thing happened when g_mindist -s was supplied with either .gro, .pdb or .tpr files. 2. Index-groups 1 and 2 consisted upon full molecules with no ommisions (full protein and not only C-alpha). 3. We ruled out PBC by using -nopi 4. This is common with the following Gromacs versions: 3.3.3., 4.0.5, 4.0.7. Regards, -Shay --gmx-users mailing listgmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
