[gmx-users] FW: protein split over boundaries
ana_j0000 at yahoo.com
Fri Apr 1 10:53:59 CEST 2011
From: anahita [mailto:ana_j0000 at yahoo.com]
Sent: Friday, April 01, 2011 1:13 PM
To: 'gmx-users-request at gromacs.org'
Subject: protein split over boundary
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
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