[gmx-users] Re: genbox - Umbrella Sampling

[Steven Neumann]

I know what is happening... I am tired :)
I used previous pdb file before moving my complex and just realised after
fighting so long, sorry for my message.

Have a good weekend,

Steven

On Fri, Feb 10, 2012 at 2:54 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> Dear Gmx Users,
>
> I am preparing my protein-ligand complex system for Umbrella Sampling
> (free binding energy of ligand) and I set
>  up the box (Pulling with Z coordinate):
>
>
> editconf -f Protein10LIGrot.pdb -o ProteinLIGbox.pdb -box 12 7 13
>
>
>
> Then using VMD I placed my Protein-Lig complex to on the right side, saved
> coordinates of the system
>
>  and tried to add water:
>
>
>
> genbox -cp ProteinLIGbox.pdb -cs spc216.gro -o Solv.gro -p topol.top
>
>
>
> The problem is that after adding water gromacs move my Protein-Lig complex
> in the center of the the Z coordinate - center my complex... Why? I want it
> as it was just before adding water. Do you have any clue what is happening?
>
>
>
> Steven
>
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