[gmx-users] question about PBC and link cell based cutoff method

linfu linfu3200 at 126.com
Wed Jun 13 09:21:53 CEST 2007

Dear GMX community!

I have question about PBC and link cell based cutoff method.

for example one water molecule,if only H atom of one water molecule
move out of box, however, O atom are still in the box. does this H atom
will need to be image back to the box through PBC,or just ignore it 
until the mass center of one water move out of the box, then use PBC to 
image back to the box. how does the gromacs do!

I am confused about the link cell based cutoff method.i read some refs about
this method,and it is very efficient.according to my understanding of precedure
step1: divide the box into NxMxL cells.
step2: put the all atoms into the cells
step3: construct the neighboring cell index.
If all the atoms do not move out of the whole box and do not apply PBC, i think 
this method is quite efficient.
Actually, we should apply the PBC for every md step, does this mean that we should
update step2 and step3 every md step. if the answer is yes, why the cell based cutoff
method is more efficient relative to sphere based cutoff.
how does the gromacs implement.

Could anyone kindly help me to figure out these question.
Thank you very much in advance!

Fu Lin 

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