[gmx-users] prolems on viewing .trr file by vmd
Mark.Abraham at anu.edu.au
Tue Apr 14 10:54:33 CEST 2009
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.
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