[gmx-users] molecule split over bounderies

ana johari ana_j0000 at yahoo.com
Fri Apr 1 10:58:14 CEST 2011

Dear user,
Hello, I appreciate if somebody help me. During the simulation of my protein I 
didn’t get any error but after 1ns of MD
my molecule was split over boundary in cubic box. it means some part of it enter 
the other side of the box.
At first,For decreasing the cost of simulation, in “editconf” command I set the 
number “d” on 0.9  to decease the box size. I want to mention that during the 
calculation my rvdw is 1.4.
I want to know instead of problem of visualization, the other things is fine?
Best regards.
A. johari
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