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

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Aug 03 2018 - 13:03:11 CDT

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>
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>
> 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>
>> 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
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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