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

[Mark Abraham]

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.

Mark

>
> 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