Software For Molecular Dynamics + Simulated Annealing = Protein Folding ?

Question

[gtrwst9]

Hello, I'm just playing with NAMD and am very impressed what CUDA can do with my nVidia graphics card. Now I have an idea about applying forces while simulating protein folding and, not wanting to reinvent the wheel, I'm asking you if there is example code for NAMD or other MD software for simulated annealing of a folding protein. Can you please point me to such code (in any language)? Bonus would be if that code could save the simulated structure in a format fit for viewing the process afterwards (PDB).

Answer 1

[Joy Ku]

You might try OpenMM. The OpenMMApplicationGuide.pdf that is available provides a sample script for simulated annealing. The software supports both CUDA and OpenCL so it can run on a variety of graphics cards.

[gtrwst9]

While this actually answers the question it also informs about a most interesting and well documented MD system that I didn't know before. Many thanks!

Answer 2

[Khader Shameer]

Have you tried GROMACS ? Check out the source code here. Also, you will be able to generate interval snap-shots from your simulation and save them as trajectory files for visualization using standard structural bioinformatics visualization tools like VMD or UCSF-Chimera.

[gtrwst9]

Thanks for your answer. It gave me the idea to search for an example using GROMACS. However, as with NAMD there are only a few crumbs of information on the combination of PC-MD software and simulated annealing. No shoulders to stand on.