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

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Aug 03 2018 - 13:55:43 CDT

Yeah. I typically use the .traj file, since you need to deconvolute based on your applied bias, which you can't determine if you change your reaction coordinate. However, if you used identical reaction coordinates, calculation from VMD and a .traj file should be identical, with the exception of the different strides used.

-Josh

On 2018-08-03 12:08:28-06:00 owner-namd-l_at_ks.uiuc.edu wrote:

Well, make sure that the same atom selections are used in each definition, otherwise you just can not compare!

On Fri, Aug 3, 2018 at 11:41 AM Rabeta Yeasmin <rabetayeasmin_at_gmail.com<mailto:rabetayeasmin_at_gmail.com>> wrote:
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.

Thanks.

Rabeta Yeasmin

On Thu, Aug 2, 2018 at 10:33 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com<mailto:giacomo.fiorin_at_gmail.com>> wrote:
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 <rabetayeasmin_at_gmail.com<mailto:rabetayeasmin_at_gmail.com>> 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
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Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
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