[gmx-users] Re: Segmentation fault in Gromacs 4.0 beta1
Hi, everyone: I am a beginner for Gromacs. I am using the latest version Gromacs 4.0 beta1. Then I follow the tutorial part: Introduction to MDhttp://md.chem.rug.nl/education/mdcourse/by the Groningen group. Compiling is ok, but I always get the Segmentation fault when I use command : genbox -cp minimized_box.gro -cs spc216.gro -o minimized_water.gro -p aki.top. Also I get the same problem when i try other exercises. Does anyone has same problem like me ? or can anyone give me a hint for that? Thanks in advance. -Xianghong Qi -- Postdoctoral Associate Department of Chemistry University of Pittsburgh Chevron Science Center 219 Parkman Avenue Pittsburgh, PA 15260 Office: 338 EBERLY Phone: 412-383-5400 Some people make the world more special just by being in it. ___ 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] Re: Segmentation fault in Gromacs 4.0 beta1
xianghong qi wrote: Hi, everyone: I am a beginner for Gromacs. I am using the latest version Gromacs 4.0 beta1. Then I follow the tutorial part: Introduction to MD http://md.chem.rug.nl/education/mdcourse/ by the Groningen group. Compiling is ok, but I always get the Segmentation fault when I use command : genbox -cp minimized_box.gro -cs spc216.gro -o minimized_water.gro -p aki.top. Also I get the same problem when i try other exercises. Does anyone has same problem like me ? or can anyone give me a hint for that? Thanks in advance. It sounds like your installation is faulty. What architecture are you running on? What compilers did you use? If you are just starting out, it is probably better to use an official release of Gromacs (the latest being 3.3.3), since 4.0beta1 is still in development. -Justin -Xianghong Qi -- Postdoctoral Associate Department of Chemistry University of Pittsburgh Chevron Science Center 219 Parkman Avenue Pittsburgh, PA 15260 Office: 338 EBERLY Phone: 412-383-5400 Some people make the world more special just by being in it. ___ 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 -- Justin A. Lemkul Graduate Research Assistant 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://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] Re: Segmentation fault in Gromacs 4.0 beta1
Thanks for your response. I followed the instruction in CVS. my architecture is x86-64, and compiler is gcc. thanks. I will try 3.3.3 -Xianghong Qi On Tue, Sep 16, 2008 at 4:02 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote: xianghong qi wrote: Hi, everyone: I am a beginner for Gromacs. I am using the latest version Gromacs 4.0 beta1. Then I follow the tutorial part: Introduction to MD http://md.chem.rug.nl/education/mdcourse/ by the Groningen group. Compiling is ok, but I always get the Segmentation fault when I use command : genbox -cp minimized_box.gro -cs spc216.gro -o minimized_water.gro -p aki.top. Also I get the same problem when i try other exercises. Does anyone has same problem like me ? or can anyone give me a hint for that? Thanks in advance. It sounds like your installation is faulty. What architecture are you running on? What compilers did you use? If you are just starting out, it is probably better to use an official release of Gromacs (the latest being 3.3.3), since 4.0beta1 is still in development. -Justin -Xianghong Qi -- Postdoctoral Associate Department of Chemistry University of Pittsburgh Chevron Science Center 219 Parkman Avenue Pittsburgh, PA 15260 Office: 338 EBERLY Phone: 412-383-5400 Some people make the world more special just by being in it. ___ 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 -- Justin A. Lemkul Graduate Research Assistant 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://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 -- Postdoctoral Associate Department of Chemistry University of Pittsburgh Chevron Science Center 219 Parkman Avenue Pittsburgh, PA 15260 Office: 338 EBERLY Phone: 412-383-5400 Some people make the world more special just by being in it. ___ 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] Re: Segmentation fault in Gromacs 4.0 beta1
Justin A. Lemkul wrote: xianghong qi wrote: Thanks for your response. I followed the instruction in CVS. my architecture is x86-64, and compiler is gcc. thanks. Be careful to use a compatible gcc version (i.e., not 4.1.x). Bad compilers can often produce nonfunctional executables. -Justin I will try 3.3.3 -Xianghong Qi On Tue, Sep 16, 2008 at 4:02 PM, Justin A. Lemkul [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: xianghong qi wrote: Hi, everyone: I am a beginner for Gromacs. I am using the latest version Gromacs 4.0 beta1. Then I follow the tutorial part: Introduction to MD http://md.chem.rug.nl/education/mdcourse/ by the Groningen group. Compiling is ok, but I always get the Segmentation fault when I use command : genbox -cp minimized_box.gro -cs spc216.gro -o minimized_water.gro -p aki.top. Also I get the same problem when i try other exercises. Does anyone has same problem like me ? or can anyone give me a hint for that? Thanks in advance. It sounds like your installation is faulty. What architecture are you running on? What compilers did you use? If you are just starting out, it is probably better to use an official release of Gromacs (the latest being 3.3.3), since 4.0beta1 is still in development. -Justin -Xianghong Qi -- Postdoctoral Associate Department of Chemistry University of Pittsburgh Chevron Science Center 219 Parkman Avenue Pittsburgh, PA 15260 Office: 338 EBERLY Phone: 412-383-5400 Some people make the world more special just by being in it. ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Postdoctoral Associate Department of Chemistry University of Pittsburgh Chevron Science Center 219 Parkman Avenue Pittsburgh, PA 15260 Office: 338 EBERLY Phone: 412-383-5400 Some people make the world more special just by being in it. -- Justin A. Lemkul Graduate Research Assistant 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://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] Re: Segmentation fault in Gromacs 4.0 beta1
I am a beginner for Gromacs. I am using the latest version Gromacs 4.0 beta1. Then I follow the tutorial part: Introduction to MD http://md.chem.rug.nl/education/mdcourse/ by the Groningen group. Compiling is ok, but I always get the Segmentation fault when I use command : genbox -cp minimized_box.gro -cs spc216.gro -o minimized_water.gro -p aki.top. Also I get the same problem when i try other exercises. Does anyone has same problem like me ? or can anyone give me a hint for that? Thanks in advance. It sounds like your installation is faulty. What architecture are you running on? What compilers did you use? If you are just starting out, it is probably better to use an official release of Gromacs (the latest being 3.3.3), since 4.0beta1 is still in development. -Justin Justin, A few days ago I experienced the same problem with genbox in gmx-4.0-beta. I didn't pay much attention to it since it's just CVS but it actually was permanently present. gmx-4.0 compiled with the same parameters on the same system does not give this error. Xianghong, There's no such problem in gmx-3.3.3 and earlier ones. I would suggest you to use them to avoid much headache. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +38-097-8259698 ___ 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
