reassignFreq expression and relation with SMD

From: Kang Hee Cho (gkdkang_at_gmail.com)
Date: Thu Mar 31 2011 - 10:56:47 CDT

• Next message: Chen, Zhihong (chenz2): "unsubscribe"
• Previous message: Francesco Pietra: "Fwd: Incompatibility between colvars and tclforces?"
• Next in thread: Matteo Rotter: "external forces"
• Reply: Matteo Rotter: "external forces"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Dear all,

I am attempting to simulate a protein(1QSU)
using SMD(steered Molecular Dynamics).
And I would you like to control temperature(300K)
using commands "reassignFreq[Temp]".

I want to know expression of command(reassignFreq[Temp])
used in NAMD.

X-PLOR use expression of velocity assignment.
(m_i/2pi/k_b/T_i)^(3/2)*exp(-3*m_i*delta^2/2/k_b/T_i)
http://www.csb.yale.edu/userguides/datamanip/xplor/xplorman/node208.html#SECTION001112000000000000000

Does NAMD use same expression?
And does reassignFreq parameter affect SMD result?

Please, could you recommend a paper or book related to
command(reassignment parameters).

Thanks and regards,
kang hee.

• Next message: Chen, Zhihong (chenz2): "unsubscribe"
• Previous message: Francesco Pietra: "Fwd: Incompatibility between colvars and tclforces?"
• Next in thread: Matteo Rotter: "external forces"
• Reply: Matteo Rotter: "external forces"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:03 CST