[gmx-users] Can I compare the force of pulling process?

[Jinzhi Tan]

Dear gmx-users:

When I tried to use steered MD to study my proteins, I encountered some problems. I have one protein with two different conformations. The ligands in the two conformations are also similar but different in details. So the two systems are not the same because the total number of the atoms (including protein, ligand and solvent)are different. My question is can I compare the pulling force between the two systems? I am not sure which factors can affect the value of the pulling force. Any suggestion will be greatly appreciated.

Best regards,

Lily Tan
2005-3-29 
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Chinese Academy of Sciences
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