[gmx-users] Problem regarding genbox

Erik Marklund erikm at xray.bmc.uu.se
Fri Jul 27 11:03:03 CEST 2007

27 jul 2007 kl. 10.44 skrev Alif M Latif:

> 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.

Are you sure they are not connected by the PBC? I really can't see  
how genbox would "push" the lipids around.


> last simulation when i used 100 nm^3 simulation box, the lipid  
> structures position and movement exceeded the box in 10 ns of MD  
> simulation.
> Suggestions and advices are greatly appreciated;
> Thank You,
> M. Alif
> Universiti Putra Malaysia
> Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s  
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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys

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