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

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
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.

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
>

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