Question on SMD simulation in spheric water .

From: cgji (cgji_at_itcc.nju.edu.cn)
Date: Fri Nov 09 2007 - 02:46:03 CST

Dear NAMD users ,

     I am trying to do Steered Molecular Dynamics simulation using NAMD .

The protein was solvated in a sphere of explicit water molecules with a radius of 32 A.

During the SMD simulation , do I need to add a harmonic restraints on the outer of the spheric water ?

 And in the SMD simulation , temperature control was turned off , and the temperature is getting higher and higher .
For extra work was imported into the system.

Do I need to care about the temperature ?

Many thanks in advance.

2007-11-09

cgji

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