Dear Maryam, I usually like to keep it simple and use gdb. That said, clang+lldb is a great compiler+debugger combo. Valgrind may also be helpful.
Kind regards, Erik > On 24 Jul 2015, at 18:02, Maryam Kowsar <maryam.kow...@gmail.com> wrote: > > Dear Erik, > > Thank you! My sleeves are rolled up for several days! Which debugger do you > suggest? > > Dear Man Hong, > > It seems we are looking at the problem from 2 different angles. Well, I am > going to test it, but I think it's not logical; without T-coupling we can't > rely on the results. However, I wonder why you think it may cause problems. > Velocities should change. I guess I can ask you questions then. Which > version of gromacs are you working with? Which source codes have you > modified? > Thank you! > > On Fri, Jul 24, 2015 at 8:41 AM, Man Hoang Viet <mhv...@ifpan.edu.pl> wrote: > >> Hi Maryam Kowsar, >> >> I have implemented external magnetic field to GROMACS and tested it. The >> code ran well and the test result is consistent with experiment for simple >> case (say Na+ in vacuum and without t_coupling). I may guest why your code >> got the error. But I am sorry that I can not share my code to anyone now >> (but I will do share it to this forum in near future). >> However, there is an important issue that MD simulation with t_coupling >> always does re-scale velocity of all atoms to keep the given temperature >> and it strongly effect on the Lorentz Force of the external magnetic >> field. Otherwise, If the t_coupling is not applied, the system temperature >> will increase forever. Therefore, I wonder whether we really can estimate >> effect of the magnetic field on protein (or other target) in simulation? >> >> >>> On 23 Jul 2015, at 11:52, Maryam Kowsar <maryam.kow...@gmail.com> wrote: >> >>> Dear users, >>> >>> Iam trying to add magnetic field code to gromacs. I think I did all the >>> modifications necessary in all source codes but when I use mdrun command >>> it >>> gives me "segmentation fault" error while in md.log the magnetic field is >>> present. When I change tpx_version the error is gone but in md.log no >>> magnetic field is implemented. How can I overcome segmentation fault >>> error? Should tpx_version be changed after adding a code? >>> >>> Thanks! >> >> Man Hoang Viet >> Institute of Physics, >> Polish Academy of Sciences. >> Al. Lotnikow 32/46 >> 02-668 Warsaw, Poland. >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
