Re: [gmx-users] segmentation fault: g_velacc
Thanks very much, Dr. Kutzner! On Tue, Feb 1, 2011 at 9:14 PM, Carsten Kutzner wrote: > Hi Vigneshwar, > > the problem is fixed now in the release-4-0-patches branch. > > Carsten > > > On Feb 1, 2011, at 2:00 PM, Carsten Kutzner wrote: > > > Hi, > > > > apparently this bug fix made it to 4.5, but not to 4.0. > > I will apply the fix also there. > > > > Carsten > > > > On Feb 1, 2011, at 1:58 PM, Justin A. Lemkul wrote: > > > >> > >> > >> Vigneshwar Ramakrishnan wrote: > >>> Dear All, > >>> I am using the gromacs 4.0.7 version and I was trying to calculate the > momentum autocorrelation function by using the -m flag. However, I get a > segmentation fault as follows: > >>> trn version: GMX_trn_file (double precision) > >>> Reading frame 0 time0.000 Segmentation fault > >>> When I don't use the -m option, I have no problem. > >>> Upon searching the userslist, I found this thread: > http://lists.gromacs.org/pipermail/gmx-users/2010-October/054813.html and > a patch, but I don't find any related bugs reported elsewhere. So, I am just > wondering if I sould go ahead and use the patch or if there could be > something else that is wrong. Will appreciate any kind of pointers. > >> > >> Either apply the patch or upgrade to a newer version of Gromacs that > contains this bug fix. > >> > >> -Justin > >> > >>> Sincerely, Vignesh > >>> -- > >>> R.Vigneshwar > >>> Graduate Student, > >>> Dept. of Chemical & Biomolecular Engg, > >>> National University of Singapore, > >>> Singapore > >>> "Strive for Excellence, Never be satisfied with the second Best!!" > >>> I arise in the morning torn between a desire to improve the world and a > desire to enjoy the world. This makes it hard to plan the day. (E.B. White) > >> > >> -- > >> > >> > >> Justin A. Lemkul > >> Ph.D. Candidate > >> ICTAS Doctoral Scholar > >> MILES-IGERT Trainee > >> Department of Biochemistry > >> Virginia Tech > >> Blacksburg, VA > >> jalemkul[at]vt.edu | (540) 231-9080 > >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >> > >> > >> -- > >> gmx-users mailing listgmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > > > > -- > > Dr. Carsten Kutzner > > Max Planck Institute for Biophysical Chemistry > > Theoretical and Computational Biophysics > > Am Fassberg 11, 37077 Goettingen, Germany > > Tel. +49-551-2012313, Fax: +49-551-2012302 > > http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne > > > > > > > > > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- > Dr. Carsten Kutzner > Max Planck Institute for Biophysical Chemistry > Theoretical and Computational Biophysics > Am Fassberg 11, 37077 Goettingen, Germany > Tel. +49-551-2012313, Fax: +49-551-2012302 > http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne > > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- R.Vigneshwar Graduate Student, Dept. of Chemical & Biomolecular Engg, National University of Singapore, Singapore "Strive for Excellence, Never be satisfied with the second Best!!" I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] segmentation fault: g_velacc
Hi Vigneshwar, the problem is fixed now in the release-4-0-patches branch. Carsten On Feb 1, 2011, at 2:00 PM, Carsten Kutzner wrote: > Hi, > > apparently this bug fix made it to 4.5, but not to 4.0. > I will apply the fix also there. > > Carsten > > On Feb 1, 2011, at 1:58 PM, Justin A. Lemkul wrote: > >> >> >> Vigneshwar Ramakrishnan wrote: >>> Dear All, >>> I am using the gromacs 4.0.7 version and I was trying to calculate the >>> momentum autocorrelation function by using the -m flag. However, I get a >>> segmentation fault as follows: >>> trn version: GMX_trn_file (double precision) >>> Reading frame 0 time0.000 Segmentation fault >>> When I don't use the -m option, I have no problem. >>> Upon searching the userslist, I found this thread: >>> http://lists.gromacs.org/pipermail/gmx-users/2010-October/054813.html and a >>> patch, but I don't find any related bugs reported elsewhere. So, I am just >>> wondering if I sould go ahead and use the patch or if there could be >>> something else that is wrong. Will appreciate any kind of pointers. >> >> Either apply the patch or upgrade to a newer version of Gromacs that >> contains this bug fix. >> >> -Justin >> >>> Sincerely, Vignesh >>> -- >>> R.Vigneshwar >>> Graduate Student, >>> Dept. of Chemical & Biomolecular Engg, >>> National University of Singapore, >>> Singapore >>> "Strive for Excellence, Never be satisfied with the second Best!!" >>> I arise in the morning torn between a desire to improve the world and a >>> desire to enjoy the world. This makes it hard to plan the day. (E.B. White) >> >> -- >> >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- > Dr. Carsten Kutzner > Max Planck Institute for Biophysical Chemistry > Theoretical and Computational Biophysics > Am Fassberg 11, 37077 Goettingen, Germany > Tel. +49-551-2012313, Fax: +49-551-2012302 > http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne > > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] segmentation fault: g_velacc
Hi, apparently this bug fix made it to 4.5, but not to 4.0. I will apply the fix also there. Carsten On Feb 1, 2011, at 1:58 PM, Justin A. Lemkul wrote: > > > Vigneshwar Ramakrishnan wrote: >> Dear All, >> I am using the gromacs 4.0.7 version and I was trying to calculate the >> momentum autocorrelation function by using the -m flag. However, I get a >> segmentation fault as follows: >> trn version: GMX_trn_file (double precision) >> Reading frame 0 time0.000 Segmentation fault >> When I don't use the -m option, I have no problem. >> Upon searching the userslist, I found this thread: >> http://lists.gromacs.org/pipermail/gmx-users/2010-October/054813.html and a >> patch, but I don't find any related bugs reported elsewhere. So, I am just >> wondering if I sould go ahead and use the patch or if there could be >> something else that is wrong. Will appreciate any kind of pointers. > > Either apply the patch or upgrade to a newer version of Gromacs that contains > this bug fix. > > -Justin > >> Sincerely, Vignesh >> -- >> R.Vigneshwar >> Graduate Student, >> Dept. of Chemical & Biomolecular Engg, >> National University of Singapore, >> Singapore >> "Strive for Excellence, Never be satisfied with the second Best!!" >> I arise in the morning torn between a desire to improve the world and a >> desire to enjoy the world. This makes it hard to plan the day. (E.B. White) > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] segmentation fault: g_velacc
Vigneshwar Ramakrishnan wrote: Dear All, I am using the gromacs 4.0.7 version and I was trying to calculate the momentum autocorrelation function by using the -m flag. However, I get a segmentation fault as follows: trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 Segmentation fault When I don't use the -m option, I have no problem. Upon searching the userslist, I found this thread: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054813.html and a patch, but I don't find any related bugs reported elsewhere. So, I am just wondering if I sould go ahead and use the patch or if there could be something else that is wrong. Will appreciate any kind of pointers. Either apply the patch or upgrade to a newer version of Gromacs that contains this bug fix. -Justin Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical & Biomolecular Engg, National University of Singapore, Singapore "Strive for Excellence, Never be satisfied with the second Best!!" I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] segmentation fault: g_velacc
Dear All, I am using the gromacs 4.0.7 version and I was trying to calculate the momentum autocorrelation function by using the -m flag. However, I get a segmentation fault as follows: trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 Segmentation fault When I don't use the -m option, I have no problem. Upon searching the userslist, I found this thread: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054813.html and a patch, but I don't find any related bugs reported elsewhere. So, I am just wondering if I sould go ahead and use the patch or if there could be something else that is wrong. Will appreciate any kind of pointers. Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical & Biomolecular Engg, National University of Singapore, Singapore "Strive for Excellence, Never be satisfied with the second Best!!" I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
