Re: [AMBER] Solvation of the membrane bilayer using tleap

From: James Starlight <>
Date: Tue, 9 Sep 2014 18:27:30 +0400

briefly the main issue here that while solvating my bilayer + protein
system using

solvatebox protein TIP3PBOX {0 0 20} 1 # to place WAT onto Z dir only

some think water layer is also added along X and Y direction
so during equilibration my system will have some changing in volume and
density ( I've noticed it only after I removed *all* restrains from the
lipids and protein)

is it possible to simply cut this bad water and define new XYZ box vectors
using tleap?


2014-09-07 11:34 GMT+04:00 James Starlight <>:

> 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 Tue Sep 09 2014 - 07:30:02 PDT
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