[gmx-users] nvt equilibration output

Mark Abraham Mark.Abraham at anu.edu.au
Wed May 16 08:30:58 CEST 2012

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 
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.


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