Generating simulation with large conformational changes

From: Shirley Hui (
Date: Sat Feb 21 2004 - 18:36:12 CST

Could someone comment on the suitability of NAMD for simulating large conformational changes in proteins? I am currently looking at the Calmodulin molecule which is known to undergo hinge like movements. In the following paper, this movement is simulated using NAMD.

They have:
* added sodium and chloride ions to the system
* used flexible water instead of rigid model
* heated the solvent to 310K then equilibrated for a period, then heated the whole system to 310K, then equilibrated, then run free MD simulation

I tried running a simulation of this protein in a waterbox solvated in TIP3 water molecules. I didn't ionize the water like they did and didn't heat the solvent separately first like they did. I am wondering which of these (or maybe all of them) need to be done to witness the same results?

I would just like to be able to see more change in structure in the protein during the simulation and wonder what needs to be done? Would it be because of their use of flexible water molecules as oppposed to rigid ones? And how do you make the water model flexible during simulation?


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