[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 <apramita.chand at gmail.com>
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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