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

[Erik Marklund]

18 okt 2012 kl. 12.08 skrev Ali Alizadeh:

> 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?
> 

The center of mass is undefined for a periodic system.

> --
> Sincerely
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html