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

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

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

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

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

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