[gmx-users] prolems on viewing .trr file by vmd

[Mark Abraham]

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