[gmx-users] Problems

pawan raghav pwnrghv at gmail.com
Sat Dec 5 16:25:20 CET 2009

When defining the box dimention then how do I know about the distance of
protein from the box wall? Which should be greater than half of the Cut-Off
(1.4nm) (according to some tutorial).

Then what are longest cutoff which must be shorter than half the shortest
box vector to satisfy the minimum image convention. I am asking because I
have run gromacs from default parameter of some other tutorial. I have used
0.75 value for -d when using editconf.

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