[gmx-users] Basic questions

[qasimpars at gmail.com]

Dear users,

I have some questions on MD simulations:

1.) I usually come accross in my GROMACS simulations: the atoms of the system jump accross the box. Why do the atoms of the system jump accross the box?

2.) In GROMACS the minimum image convention is like in this link, right?
http://www.compsoc.man.ac.uk/~lucky/Democritus/Theory/pbc-mi.html

That means that the real simulation cell surrounds with 8 boxes/cells as in the above link??

3.) Before starting simulation, I enumerate the ligand residue as a 1 (1LIG) in the starting file. After energy minimization, GROMACS renumber the ligand residue in the output gro file, e.g. 150 (150LIG). However the residue number of ligand in the ligand.itp is 1. In spite of that GROMACS doesn't give any error with the renumbered ligand 150LIG in the input file (complex.gro) for the next steps (nvt, npt and production). How GROMACS doesn't get confused with the different residue number of ligand in the ligand.itp (1LIG) and complex.gro file (150LIG)?

Any reply will be appreciated.

Thanks.