[gmx-users] genbox & protein internal H2O

[John Mercer]

Hi,

I am wanting to solvate a protein w/o adding H2O to its interior.   
Reasons:

1.  I am interested to know how the structural H2Os behave initially  
w/o interference from added H2O.
2.  Added H2O also introduce steric constraints that prevent EM from  
achieving its goal, even w/o constraints.

Have there been additional ideas since the following suggestions were  
made:

http://wiki.gromacs.org/index.php/genbox

I have no trouble identifying interior structural H2Os before  
solvation.   After solvation the visual field is cluttered w/ added  
H2O and is harder to work with.  Ideally I'd like to hide all added  
H2O outside the solvent accessible surface or perhaps a little  
farther out, and then work w/ molecular visualization.  Suggestions  
would be welcome?

A second question is that if I identify added interior H2Os and  
remove them, there will be spots in files that are not sequentially  
numbered.  Do  gromacs programs care about this?

-John