[gmx-users] distance between atoms of system and periodic image

Ester Chiessi ester.chiessi at uniroma2.it
Thu Feb 10 12:29:16 CET 2005


I'm considering a polymer network in water and I'd like to simulate a
'infinite' periodicity by covalently binding the tail of a chain with the
periodic image of its head. The network has been built with one infinite
chain in the x direction, a second infinite chain in the y direction and a
third in the z direction, to have an omogenoeous system.

The problem is that the distance between the atoms to be linked (across the
boundary) is too long in the starting structure and it's not possible to
perform the energy minimization as the bond energy is very high ( water
molecules cannot be settle ......etc).

What is the simplest way to obtain the right position of the atoms?

Sorry for my quite 'anomalous' questions and 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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