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

lsettimo at abo.fi lsettimo at abo.fi
Tue Apr 13 14:26:01 CEST 2004

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?



Luca Settimo

Department of Biochemistry and Pharmacy
Åbo Akademi University
PB 66
20521 Turku Finland

+358-2-215-4082 (work)
+358-50-5238418 (mobile)
+358-2-2154745 (fax)


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