[gmx-users] certain number of solvent molecules with genbox WITHOUT "ci"/"nmol" options

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jan 9 12:37:05 CET 2012

On 9/01/2012 9:00 PM, Vedat Durmaz wrote:
> hi guys,
> i have a molecular system that i want to simulate many times with 
> differing initial conditions, but each with the same number of 
> (solvent) atoms! i'm using gromacs 4.5.4 ...

Use different values for gen_seed. By the time you equilibrate the 
positional correlations will be lost.


> genbox with "-cs" gives me different numbers of solvent molecules.
> putting more than 20,000 tip4p molecules with the "-ci" and "-nmol" 
> combination of genbox instead runs into memory problems (40 GB is not 
> sufficient for one single system!).
> does anyone know another way of solving that issue avoiding "manual" 
> straightening?
> thanks and take care
> vedat

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