[gmx-users] pbc problem

Yang Ye leafyoung at yahoo.com
Mon Oct 15 21:48:16 CEST 2007

On 10/16/2007 2:31 AM, tangxuan wrote:
> Dear all,
>   If pbc is full or xyz in mdp file, do i need to use the "trjconv -pbc
> nojump" to remove the jump when the protein is separate in the box after
> simulation and I want to calculate the rmsd of the protein? 
IT is not necessary to use trjconv -pbc before running most gromacs 
analysis tools. they have built-in support to move atom back if they 
appear at the other side.
>  What is
> difference of use of pbc in mdp file and in "trjconv -pbc nojump"?
they are two separate stuff: specify pbc=full or pbc=xyz in mdp indicate 
that the simulation is carried out with PBC so that atoms which moves 
out of the box will appear on the other side of the box; trjconv -pbc 
nojump is a post-processing step, meant for visualization or analysis 
tools not provided by GROMACS.
> Thank you!!
> Tang Jiaowei 
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