the meaning and effect of reassignFreq and reassignTemp

From: Kang Hee Cho (gkdkang_at_gmail.com)
Date: Tue Jan 25 2011 - 08:46:39 CST

Hi, all.
Iím a NAMD user and study molecular dynamics.

I simulated the protein(1QSU) by using NAMD in 3 steps.
   First, the minimization from 0 to 2ps.
   Second, the gradually heated system during 10ps. (0K to 300K)
   Third, the equilibration during 88ps. (300K)

And then I stretched protein by using the constant velocity pulling method.

- Execution Conditions 1:
Three C-alpha of N-terminal are fixed and three C-alpha of C-terminal
are pulled.
SMDk 4.17
SMDVel 0.01 ;#0.5Angstrom/ps
reassignFreq 1
reassignTemp 300

<<<Fig. 1 >>> I linked the blog.

The above graph represent Force-displacement curve.
But I found that the force value is too high
So I commented out reassignFreq and reassignTemp.

- Execution Conditions 2 :
Three C-alpha of N-terminal are fixed and three C-alpha of C-terminal
are pulled.
SMDk 4.17
SMDVel 0.01 ;#0.5Angstrom/ps
#reassignFreq 1
#reassignTemp 300

<<<Fig. 2>>> I linked the blog.

I got the low force value in Force-displacement curve.
And I found temperature is 450K in system.
So I have several questions about reassignFreq and reassignTemp.
I have knew that if kb(Boltzmannís constant) is constant, temperature
and force are directly proportional.

<<<Appendix 1>>> I linked the blog

When I use reassignFreq and reassignTemp, the temperature is 300K in the system.
But I obtain the high force value using reassignFreq and reassignTemp.
Why is the opposite result? Could you please tell me what it means?

- Another question is how I can calculate reassigned velocity when I
use the method (reassignFreq and reassignTemp).

NAMD Userís Guide (Version 2.7) is written :
Using this method (reassignFreq and reassignTemp), all of the
velocities in the system are periodically reassigned so that the
entire system is set to the desired temperature.

In addition, I found that the pulled rate affect the force value when
using the method (reassignFreq and reassignTemp).
I would like to know the meaning and effect of reassignFreq and reassignTemp.

Thank in advance, Kang Hee.

I linked blog. You can see the Appendix and Figures.
http://blog.naver.com/gkdkang/40122152175

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