[gmx-users] Re: genconf and density of system

Thomas Schlesier schlesi at uni-mainz.de
Fri May 14 16:06:34 CEST 2010

Justin is right, the density of the real system does not always match 
the density of your force-field. If you look into the publication of the 
GROMOS 53a5 / 53a6 force-field you will see that.
For 1-butanol you get with 45a3 force-field 708kg/m^3, with 53a5 ff 
774kg/m3, and experiment tells you 806kg/m3 ...

The following command you tried
genbox –cp Hexane.gro –cs HExane.gro –p Hexane.top –o solvated.pdb
didn't work because you put your second hexane ontop of the first one.

With the option -cs genbox will use the -cs box and placeses it into the 
  -cp box. So if the -cs box is 1*1*1 nm, and you put it in a 3*3*3 box, 
you will end with 27 -cs boxes which sit next to each other, so that the 
whole box is 3*3*3 great.

Best thing you can do is, make a NPT simulation (look for the right 
compresibility) and look how much your density is off,if it's only a 
little your fine.


Message: 3 Date: Thu, 13 May 2010 17:07:31 -0400 From: "Justin A. 
Lemkul" <jalemkul at vt.edu> Subject: Re: [gmx-users] genconf and density 
of system To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Message-ID: <4BEC6A13.4010801 at vt.edu> Content-Type: text/plain; 
charset=ISO-8859-1; format=flowed Moeed wrote:
 > > Hello,
 > >
 > > I intend to generate a stack of molecules with the command line:
 > >
 > > genconf -f Hexane.gro -nbox 8 6 4 -o Hexane-STACK.gro
 > >
 > >
 > > Hexane.gro has box size of 3*3*3 nm3 and I need to have about 7
 > > molecules per nm3. So I multiplied 7 by 27 (box size) to get 
 > > molecuels. What I get from the above command is (-nbox 8 6 4 )192 but

Are you sure of that density?  If so, your box dimensions give 27 nm3, 
that you'd have to put all 189 hexane molecules in that 3x3x3 box. 
Seems a bit
crowded to me, at least for a molecule of that size.

 > > the system size in getting bigger as well!.  * 24.00000  18.00000
 > > 12.00000 nm3.*
 > >

The only thing that genconf does is build replicates of a system, it 
does not
somehow intelligently pack your system together for you, so these 
dimensions are
exactly what you would expect: (8*3), (6*3), (4*3).

 > > Could you dear experts guide me how I can reach the system density I
 > > want. Also to I wanted to know what is best value -dist option. Is 
it ok
 > > if I leave the distance between boxes 0 0 0?
 > >

I've already told you a bit about the meaning (or lack thereof) in the 
of the initial configuration.  You could conceivably simulate under a 
volume ensemble once you have a suitable configuration, but then I'd 
argue that
you're forcing the density to be right and you're not using appropriate

You can leave -dist set to zero, since the molecules are already in some 
sort of
box, and the -dist option just adds additional space between them, which is
probably not necessary.

The easiest method for building your system may simply be to decide on a 
size, determine the number of molecules that fit in it, and run:

genbox -ci hexane.gro -nmol (whatever) -box (whatever)

If all your molecules can be placed in the box, genbox will do it for you.


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