Hongyan Xiao wrote:
Dear gmx-users,
When I viewed the md trajactory (*.trr) of oil/water/oil system
using VMD, I found the trajactories are abnormal and as if there were
forces on the molecules. However, these molecules are very far. The
whole simulation is normal. How to solve this problem and obtain
the normal trajactory moving?
There will be forces between the molecules. Your trajectory will reflect
them. I don't understand what you think the problem is.
By the way, when I deal with *.gro, I used this command editconf
-f test.pdb -o test.gro -c in order to make oil/water/oil system not
turn into oil/water system. I do not know whether it effects the
following viewing trajactory moving.
Use of editconf won't affect the equilibrium state. Be aware that your
simulation box is probably periodic, and so oil/water/oil has only two
phases, not three.
Mark
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