[gmx-users] Reduction of system dimensions

James Starlight jmsstarlight at gmail.com
Mon Dec 24 10:46:17 CET 2012

So I've removed pbc from the structure and defined new box dims by
editconf. Now how I could cut all atoms which are not inclluded to
that box ( water in upper and lower leaflets) ? As I told when I did
it by means of genbox -cs b2ar_Smaller.gro -box 8.68740 8.41864
9.70145 atom order of the protein have been perturbed.


2012/12/21 James Starlight <jmsstarlight at gmail.com>:
> Hi Tsjerk!
> 1-Could the hexagonal prism be used with the membrane contained system
> ? Could you show me visual example of such pbc for bilayer-like
> systems ?
> 2-Have GROMACS build-in utilities for such deletion of the atoms
> within specified cut-offs ( e.g above or below specified distanses)
> James
> 2012/12/21 Tsjerk Wassenaar <tsjerkw at gmail.com>:
>> Tsjerk

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