[gmx-users] Re: difficulty to reproduce a box described in the literature

Pim Schravendijk schraven at mpip-mainz.mpg.de
Wed Apr 14 12:12:00 CEST 2004

It seems to me that you have an enormous amount of water molecules in 
your box! 4012 water molecules makes much more sense for a box of that 
size. How many entries do you have in  the conf.gro file, and what are the 
box sizes written at the bottom of the .gro file? 

Pim Schravendijk - PhD Student
Max Planck Institute for Polymer Research

> Message: 1
> Date: Tue, 13 Apr 2004 15:15:26 +0300
> From: lsettimo at abo.fi
> To: gmx-users at gromacs.org
> Subject: [gmx-users] difficulty to reproduce a box described in the literature
> Reply-To: gmx-users at gromacs.org
> Hello,
> I would like to run the same MD simulation described in Van der Spoel et
> al 1996 Protein Science, 5: 2044-2053.
> In the methods it is said that "the helix was solvated in a cubic box
> with an edge of ~ 5.0 nm filled with 4012 SPC water molecules"
> If I understand correct I have to specify using editconf -bt cubic and
> -d 2.5. Correct or not?
> I read that 2.5 is the distance of the protein to the edge of the box,
> in fact when I run editconf it says
> "diameter    :  4.449  (nm)"
> But then when I run genbox -cs spc216.gro it puts 26825 water molecules
> So how David obtain only 4012 SPC water molecules?
> Thanks
> Luca

More information about the gromacs.org_gmx-users mailing list