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

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 26 17:19:29 CET 2010

grivet wrote:
> 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
> g/l.
> How should I proceed to get (approximately) the desired number and
> density?

First, begin by using the right genbox flags :)  The -nmol flag is for insertion 
of extra molecules (specified in -ci).  This operation is not what you want.  If 
you wish to cap the number of solvent molecules, you want the -maxsol option.

> By the way, I notice that the number of molecules in topol.top is not
> updated; is that normal ?

Given your commands, yes.  You are not passing your topology to genbox using -p. 
  If you do, it will happily update it for you.

Also understand that the number of water molecules present in the box is 
dependent upon other species (i.e., solute).  If you are trying to compare 
results with some other system (with a different solute), the space available 
for solvent may be different, and really is an irrelevant consideration. 
Provided you have a reasonable unit cell that does not violate the minimum image 
convention, and you use the same run parameters, then the comparison should be 
legitimate.  If you simply wish to run a new simulation from a previous 
configuration, there is no need to re-build the system; just start a new 
simulation with different starting velocities.


> Thanks in advance for tour time and help
> JP Grivet


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list