[gmx-users] centering DPC micelle

T.A.Wassenaar T.A.Wassenaar at rug.nl
Thu Jun 23 21:50:48 CEST 2005

Hi Sri,

There's no such thing as a box! Ah well, maybe there is, 
but it is no more than a representation of your system, 
and everything in it is relative.

Now your problem is in representation. You see the micelle 
at the edge of a block of water, and after shifting the 
stuff, the micelle is still at the edge of the block of 
water. But that's correct. The micelle is now in the 
center of the simulation box. To get the water around it 
in a nice way, you can use trjconv with -pbc inbox. But 
for a simulation it doesn't matter.



On Thu, 23 Jun 2005 11:06:53 -0400
  VISWANADHA SRIDHARA <vsrid001 at odu.edu> wrote:
> Hi Gmx Users, I am trying to do mdrun with micelle 
>solvated in water, I have taken co-ordinates directly 
>from Tieleman's website. I found out that the micelle in 
>the original .pdb file is near the edge of the simulation 
>box. I tried to bring it to center using edit_conf -f 
>m65.pdb -o out.pdb -center, but the micelle(65DPC 
>molecules) is still at the edge of the box in the output 
>file, excepting the co-ordinates have shifted according 
>to the dimensions of the box I gave in edit_conf options. 
>Am I doing something wrong?What is the best way to bring 
>micelle to the center of the box? Thanks in Advance!Sri. 
>Graduate Research Assistant,Old Dominion 

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