[gmx-users] how to fill water molecules only in required place

[David van der Spoel]

Santan William wrote:
> Hey gmx users,
>        I just began studying gmx, here is a basic question irritating 
> me. There is a methanol.pdb ( box size: 23.619 23.619 23.619) in tutor, 
> I want to put a same size water box on the right side of methanol box to 
> simulate the mixing process. I know there is a mix.pdb file in tutor 
> already, but I want to create it by myself.  When I use genbox :
> genbox -cp methanol.pdb  -cs spc216 -o mix.pdb -box 4.7238 2.3619 2.3619
> 
> 1. The problem is, in created mix.pdb file, some water molecules always 
> inserted in methanol box. How can I just create a pdb file of left 
> methanol box only contains methanol and  right water box only contains 
> water?
> 
> 
> 2. If use "genbox -cs spc216 -o water.pdb -box 2.3619  2.3619 2.3619" to 
> create a water box, how can I get a configuration which the first atom's 
> coordinates are 0 0 0? 
> 

You have to do it manually (i.e. with a text editor). You could use 
editconf to translate one of the boxes.

> Thanks in advance.
> 
> William
> 
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se