I have simulated an elongated protein in a cubic box (reason being the long edges of the protein tilt during simulation and interact with its periodic image thus resulting in bad energy values when I had used a cuboid/triclinic box ). Now the substrate inside the protein often moves out in certain frames during the simulation. Upon visualization, I saw that the substrate molecule that moved out, is now becoming a part of its periodic image. When I do a calculation, especially like binding energy, will the substrate be rightly considered in the calculation? How can I rectify this, if it is just an imaging problem? Kindly give your valuable suggestions in this regard.
It's just an imaging problem. There's no such thing as "outside" of a periodic (infinite) system. The forces in the simulation don't care about our visualization conventions, so re-centering only matters for watching the trajectory (or in some cases, specific analyses). I doubt binding energy calculations would be affected in any way (again, the forces are fine), but you haven't said how you're calculating that quantity (during the run, post-processing, etc) so I can't say for certain.
It's just an imaging problem. There's no such thing as "outside" of a periodic (infinite) system. The forces in the simulation don't care about our visualization conventions, so re-centering only matters for watching the trajectory (or in some cases, specific analyses). I doubt binding energy calculations would be affected in any way (again, the forces are fine), but you haven't said how you're calculating that quantity (during the run, post-processing, etc) so I can't say for certain.
Yes of course, it is an imaging problem. However, if the molecule moves too fast in one direction, it may be the sign that in the system established а fluid stream. You need to pay attention to the starting conditions and correctness of algorithms that it was not happens.
Dear all,
Thank you so much for the response. I used the pbc wrap command in vmd to wrap the subsrate back to the center.
@Justin : Unfortunately, the binding energy calculations in my case were affected as I had used a processed trajectory ie which was stripped of ions and water and where only the protein was aligned . Now I am repeating my calculations with this wrapped trajectory.
Thank you all again for the response.
If you have trajectories saved, it may be much faster to write a simple program in MATLAB, Python, R, or any simple language of choice, even in Bash or csh, and re-fold the coordinates back where they should be.
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