[gmx-users] genbox

Dallas Warren dallas.warren at vcp.monash.edu.au
Wed Aug 11 00:55:02 CEST 2004

>  Now please anyone suggest how to get the distance between molecules very
>close with head to head distance very low and all the molecules being in
>same simulation box.Can I use genbox multiply and allow all the molecules
>being in same box with head to head distance what i mention.........If yes
>how,what are staements to be given.

Personally I orientate a molecule so that it is aligned along the z-axis of 
the box, so it has a small x-y profile.  Adjust the box size to something 
reasonable around the molecule, create the rough monolayer, then adjust the 
x-y dimensions to get roughly the correct area by molecule.  You can end up 
with some distorted molecules, but as soon as you do the em step they will 
straighten out.  Or even run a quick one after you have assembled it.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
When the only tool you own is a hammer, every problem begins to resemble a nail.

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