[gmx-users] nvt equilibration output

[Mark Abraham]

On 16/05/2012 4:18 PM, priya thiyagarajan wrote:
> Respected sir,
>
>  I am studying about micelle formation .. After setting box and adding 
> water i went for energy minimization and then went for nvt 
> equilibration for 1ns. when i visualized my nvt.pdb file, i found that 
> my protein comes together and formed  three micelle like structure. 
> but  my box got separated. i dono why i got two separate box.
>
> can anyone tell me why this occurs..
>
> i tried many times.. but still i am getting the same..
>
> but i already performed dynamics for 30 monomers.. that time it went 
> well.. now i am getting my output like this..
>
> i checked the system temperature.. its in equilibrium at 299.9k.

Whatever you're observing is almost certainly normal, and you need to be 
sure you understand 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions. 
The advice there, and perhaps further options you can see in trjconv -h 
will be necessary to manipulate the trajectory so that it looks the way 
you want it to.

Mark