[gmx-users] fix protein (backbone and sidechain) and equil. solvent

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 2 00:20:58 CEST 2008

Quoting t.peter.Mueller at gmx.net:

> Hi dear Gromacs users,
> I'm new to Gromacs. Sorry if this is a simple question, but I couldn't find
> anything useful via Google and co.
> >From an old simulation I have a xtc trajectory (protein without waterbox).
> I want to restart from a frame of the xtc a new simulation.
> I added to this frame all ready a waterbox.
> To avoid any "hotspots" or similar I want to run a short equilibration run
> for the water molecules and keep the protein (all atoms: backbone+ sidechain)
> fixed.
> Can anyone point me to a tutorial, example script or something similar?

What you've proposed is essentially no different than the setup for a normal
simulation.  Any tutorial will walk you through how to do a position-restrained
equilibration.  Refer to the wiki for reference:



> Thanks
> Peter
> --
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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