[gmx-users] magnetic field - segmentation fault

Maryam Kowsar maryam.kowsar at gmail.com
Fri Jul 24 19:02:54 CEST 2015

Dear Erik,

Thank you! My sleeves are rolled up for several days! Which debugger do you

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
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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