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

From: Rabeta Yeasmin (
Date: Fri Aug 03 2018 - 10:41:28 CDT

Dear Mr Fiorin,

I actually found the distances data a bit different which affects the pmf
plot shape considerably. This can be due to, as I have chosen only heavy
atoms in colvar file while the vmd script calculates the distance probably
considering all the atoms in protein and lipid. bilayer. But I am confused
which result is more reliable.


Rabeta Yeasmin

On Thu, Aug 2, 2018 at 10:33 PM, Giacomo Fiorin <>

> 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).
> Giacomo
> On Thu, Aug 2, 2018 at 5:25 PM Rabeta Yeasmin <>
> wrote:
>> 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

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2019 - 23:20:09 CST