Re: [gmx-users] g_rmsf and pbc
I tried "trjconv -pbc nojump" to the whole protein and then calculated the rmsf of the subunits. This method seems good to some separate subunits, but other separate subunits still have strange high rmsf values. I try "trjconv -pbc mol" too, and i have got same results. In this simulation,the subunits are separate in the first frame. Do you have any other methods to solve this problem? On Tue, 2007-10-23 at 17:18 +0200, David van der Spoel wrote: > tangxuan wrote: > > Mark,thanks for your reply. I am not sure what happened and I can show > > you the error message," > > Group 101 ( chK_chM) has 4070 elements > > Group 102 ( chM_chO) has 4070 elements > > Group 103 ( chO_chI) has 4070 elements > > Group 104 ( chJ_chL) has 4070 elements > > Group 105 ( chL_chN) has 4070 elements > > Group 106 ( chN_chP) has 4070 elements > > Group 107 ( chP_chJ) has 4070 elements > > Select a group: 22 > > Selected 22: 'chC' > > Reading frame 1 time 20001.000 Segmentation fault > > [miro:~/rubisco-2/chlamy_wt] % more chlamy_wt.xtc " > > Thanks. > > Tang jiaowei > > > most likely the tpr and xtc files have different number of atoms. > > as for your original problem, try trjconv -pbc mol in version 3.3.2 > > > > On Wed, 2007-10-24 at 00:43 +1000, Mark Abraham wrote: > >> tangxuan wrote: > >>> Dear all, > >>>The protein I am working on is rubisco, consisting of 8 identical > >>> large subunits and 8 identical small subunits. I try to calculate RMSF > >>> for each large subunits, but the rmsf values seems much large to some > >>> large subunits. So I check the first frame of the protein structutre, > >>> and I found that these large subunits having large rmsf values seems > >>> separate in the box. Then I tried to use trjconv -pbc nojump to remove > >>> the jump for each of them in the xtc file. When I use new xtc file and > >>> original tpr file to calculate the rmsf, it shows " Segmentation fault" > >>> error. This may be because the coordinators of atoms in the tpr file > >>> are very diffrent from that in the fist frame. Do you know how to solve > >>> this problem? > >> GROMACS does an inexplicable segfault almost never. It's highly likely > >> that either there's more of an error message than you've said, or that > >> the problem is the result some catastrophic filesystem or OS issue. > >> > >> Mark > >> ___ > >> gmx-users mailing listgmx-users@gromacs.org > >> 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 > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > 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 > > ___ gmx-users mailing listgmx-users@gromacs.org 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
Re: [gmx-users] g_rmsf and pbc
tangxuan wrote: Mark,thanks for your reply. I am not sure what happened and I can show you the error message," Group 101 ( chK_chM) has 4070 elements Group 102 ( chM_chO) has 4070 elements Group 103 ( chO_chI) has 4070 elements Group 104 ( chJ_chL) has 4070 elements Group 105 ( chL_chN) has 4070 elements Group 106 ( chN_chP) has 4070 elements Group 107 ( chP_chJ) has 4070 elements Select a group: 22 Selected 22: 'chC' Reading frame 1 time 20001.000 Segmentation fault [miro:~/rubisco-2/chlamy_wt] % more chlamy_wt.xtc " Thanks. Tang jiaowei most likely the tpr and xtc files have different number of atoms. as for your original problem, try trjconv -pbc mol in version 3.3.2 On Wed, 2007-10-24 at 00:43 +1000, Mark Abraham wrote: tangxuan wrote: Dear all, The protein I am working on is rubisco, consisting of 8 identical large subunits and 8 identical small subunits. I try to calculate RMSF for each large subunits, but the rmsf values seems much large to some large subunits. So I check the first frame of the protein structutre, and I found that these large subunits having large rmsf values seems separate in the box. Then I tried to use trjconv -pbc nojump to remove the jump for each of them in the xtc file. When I use new xtc file and original tpr file to calculate the rmsf, it shows " Segmentation fault" error. This may be because the coordinators of atoms in the tpr file are very diffrent from that in the fist frame. Do you know how to solve this problem? GROMACS does an inexplicable segfault almost never. It's highly likely that either there's more of an error message than you've said, or that the problem is the result some catastrophic filesystem or OS issue. Mark ___ gmx-users mailing listgmx-users@gromacs.org 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 ___ gmx-users mailing listgmx-users@gromacs.org 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org 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
Re: [gmx-users] g_rmsf and pbc
Mark,thanks for your reply. I am not sure what happened and I can show you the error message," Group 101 ( chK_chM) has 4070 elements Group 102 ( chM_chO) has 4070 elements Group 103 ( chO_chI) has 4070 elements Group 104 ( chJ_chL) has 4070 elements Group 105 ( chL_chN) has 4070 elements Group 106 ( chN_chP) has 4070 elements Group 107 ( chP_chJ) has 4070 elements Select a group: 22 Selected 22: 'chC' Reading frame 1 time 20001.000 Segmentation fault [miro:~/rubisco-2/chlamy_wt] % more chlamy_wt.xtc " Thanks. Tang jiaowei On Wed, 2007-10-24 at 00:43 +1000, Mark Abraham wrote: > tangxuan wrote: > > Dear all, > >The protein I am working on is rubisco, consisting of 8 identical > > large subunits and 8 identical small subunits. I try to calculate RMSF > > for each large subunits, but the rmsf values seems much large to some > > large subunits. So I check the first frame of the protein structutre, > > and I found that these large subunits having large rmsf values seems > > separate in the box. Then I tried to use trjconv -pbc nojump to remove > > the jump for each of them in the xtc file. When I use new xtc file and > > original tpr file to calculate the rmsf, it shows " Segmentation fault" > > error. This may be because the coordinators of atoms in the tpr file > > are very diffrent from that in the fist frame. Do you know how to solve > > this problem? > > GROMACS does an inexplicable segfault almost never. It's highly likely > that either there's more of an error message than you've said, or that > the problem is the result some catastrophic filesystem or OS issue. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > 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 ___ gmx-users mailing listgmx-users@gromacs.org 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
Re: [gmx-users] g_rmsf and pbc
tangxuan wrote: Dear all, The protein I am working on is rubisco, consisting of 8 identical large subunits and 8 identical small subunits. I try to calculate RMSF for each large subunits, but the rmsf values seems much large to some large subunits. So I check the first frame of the protein structutre, and I found that these large subunits having large rmsf values seems separate in the box. Then I tried to use trjconv -pbc nojump to remove the jump for each of them in the xtc file. When I use new xtc file and original tpr file to calculate the rmsf, it shows " Segmentation fault" error. This may be because the coordinators of atoms in the tpr file are very diffrent from that in the fist frame. Do you know how to solve this problem? GROMACS does an inexplicable segfault almost never. It's highly likely that either there's more of an error message than you've said, or that the problem is the result some catastrophic filesystem or OS issue. Mark ___ gmx-users mailing listgmx-users@gromacs.org 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
[gmx-users] g_rmsf and pbc
Dear all, The protein I am working on is rubisco, consisting of 8 identical large subunits and 8 identical small subunits. I try to calculate RMSF for each large subunits, but the rmsf values seems much large to some large subunits. So I check the first frame of the protein structutre, and I found that these large subunits having large rmsf values seems separate in the box. Then I tried to use trjconv -pbc nojump to remove the jump for each of them in the xtc file. When I use new xtc file and original tpr file to calculate the rmsf, it shows " Segmentation fault" error. This may be because the coordinators of atoms in the tpr file are very diffrent from that in the fist frame. Do you know how to solve this problem? Thank you Tang Jiaowei ___ gmx-users mailing listgmx-users@gromacs.org 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
