[gmx-users] During mdrun my protein moves towards edges

Diogo Vila Viçosa diogo.vicosa at fc.ul.pt
Mon May 11 11:26:17 CEST 2015

You do not have a "problem" you only have the "normal" protein diffusion.

Take a look in trjconv tool.


Option -center will be your best friend I guess.

Diogo Vila-Viçosa

Em seg, 11 de mai de 2015 às 10:14, Seera Suryanarayana <palusoori at gmail.com>

> Dear gromacs users
> I have been running the real mdrun after equilibration. mdrun has been
> submitted for 500ns. After some time(150ns) the protein moves towards
> edges. I want the internal moments only, but whole protein moves all sides
> of box rather than at centre of the box. Kindly tell me how to overcome
> above mentioned problem and what could be the reason?
> Thanks in Advance
> Surya
> Graduate student
> India.
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