[gmx-users] PBC

[Justin Lemkul]

On 2/12/18 8:44 AM, Ahmed Mashaly wrote:
> Hi
> If I want to use gmx trjconv to recenter the protein in xtc file, the reference (-s) .tpr should be the one I used in simulation (md.tpr) or I can use the first one (em.tpr) without a difference?
>
> This is because the protein has jumped after em step, and if I have to use md.tpr as reference for md.xtc, I will have to recenter it after every step of em, nvt, npt

You can use whatever reference coordinates you want. Energy minimization 
generally shouldn't result in large structural changes, so make sure you 
have a sufficiently large box to avoid spurious minimum image interactions.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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