minimization temperature and constraints

From: AYTUG TUNCEL (ATUNCEL_at_KU.EDU.TR)
Date: Tue Dec 05 2006 - 17:20:22 CST

Dear all,

I have some basic questions about minimization procedure,

1) What is the difference between keeping the protein (at least the CA atoms) fixed or relaxed during minimization? For ex. What is the purpose of keeping the portein fixed while heating up the system (say from 0K to 310K)?

2)If I want to provide a uniform density for water molecules in the box, should I couple NPT with heating up process or do the NPT after reaching the desired temperature (310K) ?

3)In NAMD usersguide there is this parameter "reinitvels". What is the difference between using this parameter or manualy increasing the temperature (heating up the system) after minimization?

Thanks in advance.

Aytug

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