[gmx-users] pbc problem
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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