[gmx-users] water box with prescribed volume and density

grivet grivet at cnrs-orleans.fr
Fri Mar 26 16:26:44 CET 2010

Hello Everybody,

As a Gromacs newby, I am trying to simulate a box of water (under
gromacs4.0.5). I did the following:

	pdb2gmx -water spce -f spc216.pdb
	genbox -cs conf.gro -box 5.1 5.1 5.1 -nmol 4412 -o eau270.gro

I have the following constraint; I wish to compare results with a
previous simulation done with Gromos, using 4412 molecules in a
5.1x5.1x5.1 cubic box. 

However, genbox will not let me do this; it places some 3400 molecules
in the box, with a very low density, 828 g/l. If I do

	genbox -cs conf.gro -box 6 6 6 -nmol 4412 -o eau270.gro

then I get 5600 molecules in the box, with an even lower density of 808
How should I proceed to get (approximately) the desired number and
By the way, I notice that the number of molecules in topol.top is not
updated; is that normal ?
Thanks in advance for tour time and help
JP Grivet

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