[gmx-users] RE: I want to add 460 molecules into a box

Dr. Vitaly Chaban vvchaban at gmail.com
Tue Oct 9 12:00:14 CEST 2012

> I want to add 460 molecules into a box but i can not add more than 400
> molecules,
> genbox -ci het.gro -nmol 460 -box .......
> Even, when i change VanderWaals radii( i reduce it,vdwwradii.dat ) but
> maximum molecules to be 440.
> Decrease more than it, atoms overlap,
> How to can i add my number of molecules(460) into system?

If you WANT to add, you SHOULD add, otherwise, you will become frustrated.

1. Increase the size of the box. editconf or genbox can be that.
2. Decrease the default VDW radius, while using genbox, and further
run energy minimization procedure, see grompp.mdp.
3. There are more fancy ways, e.g. run your system at sufficiently
high temperature to decrease the density and create voids. Then you
will get more space for new particles to occupy.

The first routine will be less troublesome, unless you want to
preserve the initial geometry of the system.

Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark

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