Thank you Erik! On Sun, Jul 26, 2015 at 2:49 AM, Erik Marklund <erik.markl...@chem.ox.ac.uk> wrote:
> 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. > -- 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.