Dear Amber users!
I have a problem with the adding water to the lipid bilayer (with the
embedded protein) using tleap commands.
In my case I need to add water only along Z direction from upper and
bottom parts of the bilayer. Using the below command to much water has been
added (including some water from the x and y):
solvatebox protein TIP3PBOX {0 30 0} 1
so in the npt equilibtation my system has been non stabile due to the high
perturbations in its total volume
alternatively
solvatebox protein TIP3PBOX {0 30 0} 2
produced alot of space betwen polar groups of the lipids and water.
Is it possible to make solvation better? (e.g in gromacs there were a trick
to modify vdw radii during the solvation to avoid such voids)
Thanks for help,
James
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Received on Sun Sep 07 2014 - 01:00:02 PDT
