[gmx-users] Fwd: I have a symmetric simulation box,

Ali Alizadeh ali.alizadehmojarad at gmail.com
Thu Oct 18 12:08:42 CEST 2012

Dear All users

1- I have a symmetric simulation box but i can not produce a symmetric
number density result (number density vs. z direction(nm))

My simulation box is orthorhombic. My boundary condition is pbc but i
don't perform any commands before final run for

Preparation of simulation box(related to pbc) and Just, in my input
file(.mdp file) select  pbc xyz-option.

     1- construction of simulation box with a software
     2- pdb2gmx for producing .gro and .top
     3- energy minimization
     4- nvt(it converged)
     5- npt(it converged)
     6- production of md(2 nano second)

2- I don't locate the centre of masses. How can i  determine it?Is it necessary?


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