[gmx-users] Optimizing system size by moving from rectangular to hexagonal cells

[Mark Abraham]

----- Original Message -----
From: 张春雷 <chunleizhang.pku at gmail.com>
Date: Friday, June 25, 2010 18:06
Subject: Re: [gmx-users] Optimizing system size by moving from rectangular to hexagonal cells
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> I think you may try "trjconv -ur".

I don't think that can work, because the OP needs to remove a subset of molecules, and trjconv -ur can't do that. I am not aware of any GROMACS tool that might serve the purpose. I suspect the only reasonable solutions are to equilibrate the hexagonal cell from scratch, or to write a script to apply the new unit cell boundaries, and then re-equilibrate.

Mark

> 2010/6/25 Marc Baaden <baaden at smplinux.de>
 > 
>  Dear All,
 > 
>  Trying to optimize some simulation systems, I noticed that I could
>  actually gain quite some degrees of freedom by changing the xy
>  dimension of my simulation system from square/rectangular to hexagonal.
>  I wonder how one would do that in order to preserve at best the
>  properties of an already equilibrated system with a rectangular
>  xy-plane. Can Gromacs simply "cut" a hexagonal patch out of a periodic
>  simulation box with rectangular geometry?
>  Which tool would one use for this task? Editconf, with options eg
>  -c -box a b c -angles 120 120 90 ?
 > 
>  Thank you very much in advance,
>    Marc Baaden
 > 
>  --
>   Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
>   mailto:baaden at smplinux.de      -      http://www.baaden.ibpc.fr
>   FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217
 > 
 > 
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