[gmx-users] Different results for same protein's simulation in 4.6.5 and 5.0.4

[Dries Van Rompaey]

On 29 February 2016 at 08:48, SAPNA BORAH <sapnauser365 at gmail.com> wrote:

> hi
> Thanks for the suggestion. I will give this a shot, and remove these
> restraints.
>
> I am unclear about what should I be looking in the log file as you
> mentioned. The conformations are not just close, they are the same as the
> initial conformation.
>
See if you can find "Position rest." in your logfile in the Energies
subsection.


>
> I have some understanding on pbc that serves a problem in visualisation of
> the trajectory. I have applied the all sorts of pbc options, but somehow
> things are not falling into place.


If you could post a screenshot of what it looks like that would be handy.
Currently there's not much else I can tell you.


>
>
However the problem more grave here, for me, is the production run and the
> model stability that is happening throughout the simulations in different
> versions.
>
> The model stability is probably caused by the postion restraints. If
you're telling gromacs to apply a restraint that penalizes movement of your
atoms, it makes sense that you won't be seeing much movement.