NAMD in water vs in vacuum

From: Yang Gao (
Date: Thu Jun 05 2008 - 09:54:48 CDT

Dear all,

I am a little confused about the namd running for a big protein in a water box
or in vacuum. I have read some papers that they used vacuum simulation and said
it is no big difference with the running with water.
 In my case for a ~900 residue protein, the running in the vacuum (with all the
structural waters in the original pdb file) caused two domains coming together
and a salt bridge formed, while in the original crystal structure, there are
more space between and of course occupied by the solvent. But in a short run in
water box i did not see this conformational change.
 I know it should take much more time for a conformational change in solvent
than in vacuum and i may need a longer run, but it may take me and the computer
too much time. So I am quite interested if it is a real-happened thing or just
because i removed the solvent, and how much longer time it will take for a
conformational change in water box if it will happen for generally speaking. Is
there any report published about this kind of difference in vacuum vs in solvent?

Thank you very much.

 Yang Gao

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