[gmx-users] Re: Extending water in negative Z direction

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jun 5 08:43:59 CEST 2009


Please, many of us have years of experience with MD and this type of
systems. If you had considered that, rather than assuming that we
still don't understand what you mean, you would have been on the right
track to fix an apparent caveat in your knowledge regarding MD
simulations, and notably periodic boundary conditions. Your system is
periodic. That means that one side of your box is equal to the other
side. You have an infinite system, or a wrapped system. In the
coordinate file you maybe see something that can be represented as:


Where P is your protein, the dashes represent the water layer and the
vertical bars represent the box edges. But under PBC that means you

|P------||P------||P------||P------| etc

Now you can't see the box edges in such a system, so it's exactly like having


And that means you have water on both sides of the protein. You can
shift the system a bit and take one part out:


It's exactly the same thing! There just isn't another side in a periodic system.

As Justin pointed out, this is one of the very basic aspects of MD
simulations. It is vital to understand it before starting simulations,
and you should not try and go for expert topics like simulations of
GPCRs in membranes before mastering the basics.

I hope this makes things clear.



On Fri, Jun 5, 2009 at 8:25 AM, Anirban Ghosh<anirbanz83 at yahoo.co.in> wrote:
> Hi ALL,
> Thanks for the reply. I think what I mean will be more clear by just having
> a look at the structure (attached). I have tried by increasing the Z value,
> as suggested by David, but that only extends the water on one side of the
> bilayer only and not on the other side (which I need). Please have a look at
> the structure.
> Thanks a lot.
> Regards,
> Anirban Ghosh
> Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
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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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