Re: [gmx-users] Should the peptide be centered initially in the box if we want to calculate its diffusion later?

[Mark Abraham]

Hi,

There's no center of a periodic cell, so wherever you place it originally
is arbitrary. You get restraints only if you choose to have them in your
topology.

Mark

On Tue, Jun 27, 2017 at 9:00 AM Apramita Chand 
wrote:

> Dear All,
> Using g_editconf, I am centering the peptide in the box initially. During
> equilibration, I'm gradually releasing position restraints. I want the
> peptide to be free to move around so that I might calculate its diffusion
> constant.
> In that case, will centering using -c option restrain its motion ?
>
>
> yours sincerely
> Apramita
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Re: [gmx-users] Should the peptide be centered initially in the box if we want to calculate its diffusion later?

[Nikhil Maroli]

Hi Apramita,

Up to my knowledge, It is not necessary to keep the peptide at the centre
due to the periodicity you can have 'continues' motion throughout the
simulation. But, it is always better to keep it in convenient positions to
avoid any artefacts. Further, I don't have any idea about your simulation
system, whether it contains lipid layers or any other proteins and what
kind of motions/diffusions your expecting.
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[gmx-users] Should the peptide be centered initially in the box if we want to calculate its diffusion later?

[Apramita Chand]

Dear All,
Using g_editconf, I am centering the peptide in the box initially. During
equilibration, I'm gradually releasing position restraints. I want the
peptide to be free to move around so that I might calculate its diffusion
constant.
In that case, will centering using -c option restrain its motion ?


yours sincerely
Apramita
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