I am trying to solvate a bunch of cellulose chains with waters using gmx solvate. but it seems that no matter what I do, there will be water molecules (shown in yellow) “in between” the cellulose chains (shown in cyan) since the chains are sufficiently far away from each other. Is there a good way for me to force the solvation to happen only “outside” of the entire packed cellulose structure (outside the outmost cellulose chains)?
Or equivalently, is there a way for me to specify a minimum distance between solute and solvent during solvation without messing up the water density (meaning not using gmx solvate -scale)? If so, I can simply define a larger value for this minimum distance.
Thanks in advance!
. A database (vdwradii.dat ) of van der Waals radii is read by the program, and the resulting radii scaled by -scale . If radii are not found in the database, those atoms are assigned the (pre-scaled) distance -radius .
This seems to suggest that -radius only has an effect when the vdW radii of the atom is not found in the database, but my atoms are just C, H, and O which are all in the database already. Did I misunderstand something over here?
