[gmx-users] simulation box

[Anton Feenstra]

Nguyen Hoang Phuong wrote:
> 
> Dear All,
> 
> Does anyone know how to create the simulation box which contains peptide
> and water at the given box size and the number of water molecules? What I
> have done is that I specify the density (corresponding to the voluum and
> the number of water molecules) in the program editconf but when I use the
> program genbox, he gives me default value of the density. Thanks for your
> help in advance.

There is no straightforward solution to your problem.
First, let me explain a bit. The -density option to editconf simply
scales your coordinate file to get the requested density (as the
manual says). This has no effect on the density of the water box that
genbox produces, since that is determined by the density of your
input water box (usually this is the default spc216.gro, which is
1kg/l density). 

If you want a water box at a different density, you can do several 
things:
1) first scale the spc216.gro, for example using the -density option
of editconf and then solvate your peptide in the resulting water.
2) solvate your peptide in the default spc216.gro water, and select
a box size to get the desired amount of water and then scale the
system to the desired density.
Both will scale the whole system, including e.g. bond lengts.
This may or may not be a problem (energy minimization and/or 
constraints, e.g. Lincs or Shake, will fix most of it), and will
probably each have their own problems. 
More variants are possible, I leave that to your imagination.

Hope this helped you a bit... ?

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
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