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
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