[gmx-users] simulation confined to a small region

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Feb 23 07:46:35 CET 2007

Hi Filip,

You first really have to ask yourself what question you want to
answer. A protein is a mechanical construct and the greater part of
the protein is not just there for decorative purposes. Even the
interactions between two close by residues will be tied in with the
dynamics of the rest of the system. Constraining or even chopping of
the part you think you're not interested in will likely alter the
dynamics of the portion you are interested in so much that you start
to wonder whether what you see has any (physiological) relevance at


On 2/23/07, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> > Has anybody had success on running a simulation on only a part of a
> > protein? I have a very large protein, and I'm only concerned with
> > analyzing the motions of two specific close sidechains rather than
> > analyzing the complete system. Do you recommend that I set the simulation
> > box to very very small dimensions and then orient the box so that the two
> > side chains are in the center of the box? If that's how it is done, I've
> > had no luck with using editconf. Any suggestions?
> This problem is closely confounded by how you want to treat the region of
> the protein you're planning to chop off. Periodic boundary conditions are
> useless to you, unless you take enough of the protein that you think it's
> electrostatic interactions with these sidechains is well-enough covered,
> use position restraints as appropriate on that protein fragment, cap the
> inevitable bits of sequence that will be dangling, and then take at least
> two complete solvation layers around the whole lot - since the water
> structure near the former "inside" parts of the protein will be weird.
> An alternative is to do "shell MD", where you again pick a reasonable
> chunk of your protein, cap bits of it, use position restraints and/or
> fixed atoms, introduce a solvent layer around the sidechains, and then
> another solvent layer around that with PR and fixed atoms, wide enough
> that the electrostatic effect of the vacuum outside is probably
> negligible.
> In the former case, editconf will be no use to you until you've built the
> system by hand with some other tool. In the latter case, I can't see
> editconf being of use at all.
> Mark
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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