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

From: Giacomo Fiorin (
Date: Thu Aug 02 2018 - 22:33:16 CDT

When calculated on the same configurations (coordinates + unit cell), the
numbers should be identical save for the difference in the last digits
(NAMD uses double precision, but trajectory files are in single).


On Thu, Aug 2, 2018 at 5:25 PM Rabeta Yeasmin <>

> 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

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD

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