[gmx-users] condensing

Dallas Warren dallas.warren at vcp.monash.edu.au
Mon Mar 15 00:23:00 CET 2004


>i was just curious, but do any of the programs with gromacs allow me to
>condense a simulation? what i mean by this is that i am running a
>simulation with 40 lipids and 3000 water molecules in a box at approx. 64
>A/lipid. i want to reduce this to 50 A/lipid. thanks.

If you aren't using pressure coupling along the membrane, i.e. x-y, then 
simple change the box dimensions as required to give the needed cross 
sectional area.  editconf has a -scale option, so you can scale the x and y 
dimensions in the box by that amount.

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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