about recentering of namd trajectory

From: zhangliqun (lqzhang0332_at_hotmail.com)
Date: Tue Aug 17 2010 - 10:50:54 CDT

• Next message: Kwee Hong: "problem at maintaining geometry coordinate"
• Previous message: Giacomo Fiorin: "Re: Umbrella Sampling Methodology"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Dear NAMD administrator:

I ran protein complex simulations (one protein with one small gtpase) using NAMD software. In the input file, I used wrapall on settings. In analyzing the rmd based on the trajectory, I found very large values of msd for the complex after align the frame orientation to the initial position. I tried to use chamm code to do recentering on the trajectory, but no improvement. Could you give me some idea on how to solve that? Thank you very much.

Best regards,

Liqun Zhang
                                               

• Next message: Kwee Hong: "problem at maintaining geometry coordinate"
• Previous message: Giacomo Fiorin: "Re: Umbrella Sampling Methodology"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:03 CST