From: Kang Hee Cho (gkdkang_at_gmail.com)
Date: Tue Jan 25 2011 - 08:46:39 CST
Hi, all.
I’m 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(Boltzmann’s 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 User’s 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
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:19:44 CST