Which one is more reliable to use in umbrella sampling- .traj data or vmd script data

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Thu Aug 02 2018 - 16:24:35 CDT

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Dear NAMD users,

I have run umbrella sampling of a protein-lipid bilayer in NAMD. I have
restrained the z-distance between the heavy atoms of the protein and lipid
bilayer. I have got distance data from two sources- one from .traj file
produced during NAMD simulation and another one is from vmd script to get
mass center distance of protein and lipid bilayer. After combining those
datas in WHAM, I found that those two sources of data gives different
result. I am wondering which one will be more reliable to use in WHAM.

Thanks.

Rabeta Yeasmin

• Next message: Giacomo Fiorin: "Re: Which one is more reliable to use in umbrella sampling- .traj data or vmd script data"
• Previous message: Sadegh Faramarzi Ganjabad: "Re: Rattle error with lateral pressure calculations"
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