[gmx-users] problem with g_density -center

Justin A. Lemkul jalemkul at vt.edu
Sun Aug 21 00:54:53 CEST 2011

Sanku M wrote:
> Hi,
>   I am trying to calculate the density profile of  head group of bilayer 
> normal to z direction using gromacs 4.0.7. I was trying to center the 
> density profile about dx/2.dy/2,0 . But, I am finding problem with using 
> center option. I find using -center option does not shift the bilayer to 0. 
> The following was my command-lines:
> g_density_4mpi -f ../traj_npt -s ../topol -noxvgr -n ../index -b 600000 
> -dens number -center -o density_phosphate_symm.xvg
> Any help on how to use the center option will be really helpful.

For this purpose, trjconv is more reliable.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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