[gmx-users] Reduction of system dimensions

James Starlight jmsstarlight at gmail.com
Fri Dec 21 08:23:54 CET 2012

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 ?


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