[gmx-users] Re: genconf and density of system
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
somehow intelligently pack your system together for you, so these
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
> > 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
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
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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