[gmx-users] constraining distance and minimum image convention

Ester Chiessi ester.chiessi at uniroma2.it
Tue Feb 8 12:24:28 CET 2005


I'd like obtain a certain distance (and eventually orientation) between two
atoms (A, B) of my system in the simulation box.
The distance between B and one of the periodic images of A is very shorter
than the distance between the two atoms inside the box.
Which value of distance do I have to consider for the constraint, if I work
in periodic boundary condition?

In particular, if I start with a distance (between atom inside the box) too
long and I use the pull code in constraint mode, shell I give a negative
constraint_rate ( or positive, to shorten the distance with the periodic

Thanks in advance


Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Università di Roma Tor Vergata
Via della Ricerca Scientifica
00133 Roma
tel. +39 06 72594462
fax  +39 06 72594328

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