[gmx-users] magnetic field - segmentation fault

[Maryam Kowsar]

Thank you Erik!

On Sun, Jul 26, 2015 at 2:49 AM, Erik Marklund <erik.marklund at 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.kowsar at 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 <mhviet at 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.kowsar at 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.
> >>
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