[gmx-users] Re:Question regarding

[Vitaly Chaban]

>>Because GROMACS is a great software.
>  Thanks for the reply, what may be the reason GROMACS became great?

Please see the tutorial as for algorithms for non-bonded interactions
in gromacs.


>> > 2.If do minisation while running shows that
>> >   Back Off! I just backed up step53.pdb what may be the reason?
>>
>>The system is exploding.
>  sometimes though system explodes it will generate energy minimisation output.gro file we cant use this file for further run?

If the system is exploding the right way will be to re-initialize it
(or just add the part causing the problems) from the very beginning to
be sure everything is correct.

-Vitaly