[gmx-users] distance restraints and periodic image
hritz at tom.fos.su.se
Mon Sep 2 10:08:47 CEST 2002
I use distance restraint inside "one molecule" which consists of two parts
A, B. Normal distance restraint lenght is 0.5 nm. During MD everything is
OK until part A jump to its periodic image and distance restraint is
applied between B in original box and A in next periodic cell. Now
distance lenght is 3 nm and very strong (artificial) force between A B is
applied. B in original box is moving to A in next box.
How to apply normal distance restraint between A, B in original box?
I also don't understand why A jump to its periodic image, when only small
part of it is out of box. Is there opportunity let A in original box
during whole MD? (I am not talking about visualisation)
Thank You very much
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