[gmx-users] Problem regarding genbox

Alif M Latif prism_dead at yahoo.com
Fri Jul 27 10:44:50 CEST 2007

Dear GROMACS Community,

I'm having problem adding spc water molecules into my system containing lipids molecules totaling 64 of them. My simulation box size is 1000 nm^3. I told genbox to fill the simulation box with 100 nm^3 of spc216 water molecules using option (-box 4.642 4.642 4.642)  due to the experimental formulation of the mixture. 

unfortunately, when i view the system, the 100nm^3 of spc216 water that i fill into the box pushed my lipids to each corners of the simulation box. Should i proceed with the simulation or can somebody tell me how to avoid this from happening? Because if the lipids region is at each of the corners, i'm worried about the hydrophobic effect of the lipid structures which i want to study. I wanted the system to be in the box, and the molecules are randomly scattered. 

last simulation when i used 100 nm^3 simulation box, the lipid
structures position and movement exceeded the box in 10 ns of MD

Suggestions and advices are greatly appreciated;

Thank You,
M. Alif
Universiti Putra Malaysia

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