[gmx-users] Reduction of system dimensions

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Dec 21 08:33:31 CET 2012

Hi James,

It's probably better to put all the molecules in the original box (trjconv
-pbc mol), and then delete all molecules with an atom with z<0 or z>9.7. In
addition, why not use a hexagonal prism to limit the size of your system
further? Saves and additional 14%.

Hope it helps,


On Fri, Dec 21, 2012 at 8:23 AM, James Starlight <jmsstarlight at gmail.com>wrote:

> Dear Gromacs users!
> I have a protein embedded in membrane surrounded with 2 uipper and
> lower water leafleates. I decide to decrease number of water in that
> system (in both leafletes) by reducing its size in Z-dimension.
> Firstly I've defined new box vectors of my system via editconf and
> than I've uded genbox to cut water in both upper and lower leaflets
> genbox -cs b2ar_Smaller.gro -box 8.68740 8.41864 9.70145
> here 9.70145 is the new size of the Z dim (vs 12.0 in old version.
> That produce system with desireble water\lipid ratio but atom order in
> protein was perturbed. How I could fix such problem or reduce system
> size by different methods ?
> James
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4

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