For molecular dynamics you need more memory. I ran MD for a protein and it took 4 days to finish in a 64 gb ram computer.

Chimera usually used for the visualization purpose. you may have to try gromacs or namd

Samee Ullah Thanks for your response. The problem is I am not from CS background and GROMACS does not run in Windows OS (easily). Even I have tried to install it in Ubuntu but failed. :)

This is a common issue when you use chimera for minimization and MD. all you need is to wait for results "Not responding "doesn't mean it doesn't run". Since you are not from CS background ,Get used to NAMD alongwith VMD. This has got quickMD extension for Novices which might help you.

Wait means sometime for days, programs are designed not to respond while performing lengthy calculations, Once the calculation is done it will start responding again.

Venkataraghavan Can you please let me know the detail how to run MD simulations of protein-ligand complex using Chimera.

It's not advisable to run MD on chimera interface. Chimera is just good visualizer and can work with plugins like modeller, autodock etc. Just install Gromacs on windows as per earlier suggestions (@samee ullah) or compile it through cygwin. Another easy way in windows is to install virtual box and ubuntu OS. I havn't found any other easier way than to use Gromacs or other MD programs through linux or cygwin commands.

Regards

Hello, everyone..I got the same issue as I begun a MD it finished and then got to "Not responding mode", but I understand and still waiting for it to finish. I got VMD/Namd2 for MD, yet I do really enjoy the graphics and analysis interface of Chimera. Question is Can I run MD in VMD/Namd2 and do analysis on Chimera? How can I import MD data from VMD into Chimera? Thanks.