SMD of proteins in water box without PBC

From: dora guzman (dguzman_at_uci.edu)
Date: Wed Jul 04 2007 - 11:56:46 CDT

Hello,

I have been following Schulten¹s work on SMD of proteins. His earlier work
used proteins in a waterbox without periodic boundary conditions. Basically,
the water molecules followed the trajectory of the stretched atoms. How
might this affect the simulations when compared to systems fully solvated
and using PBCs (other than higher forces)? Also, how big should the waterbox
be to obtain decent results? Their more recent work uses a huge water box to
keep the protein solvated when fully stretched, but they also have access to
hundreds of processors. This method would not be computationally feasible
for me.

Currently, I have a protein that is 167 residues long solvated in a water
box‹ total number of atoms of the system: 70,423
SMD is being carried out without PBC, but the resulting Force-extension
curves show very high forces (~5000 pN).

Any information would be greatly appreciated.

Thanks.
-dora

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