[gmx-users] magnetic field - segmentation fault

[Erik Marklund]

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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