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
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