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.
