[gmx-users] About Removing excees Water molcules in Lipid Bilayer simulation

Justin Lemkul jalemkul at vt.edu
Sun Oct 28 14:32:57 CET 2012

On 10/28/12 8:50 AM, vidhya sankar wrote:
> Dear justin,
>                   Thank you For your Previous reply
> I  am doing Lipid -protein  Bilayer simulation.  As instructed in your tutorial i Have done Shrinking And  EM .until i have Attained Area per Lipid 62.36A. Then I Have solvated  as in the Tutorial (  using Vadradii 0.375)  using Genbox tool
> As result My system has Solvated with 74496 Solvent Molecules . This is Too Higher for My system
> Is there is any  Gromacs tools or other server or Package  Available to delete  Excess Water molecules . I wanted to Keep Water Molecules only on Either side of Bilayer  While  I need to Delete  Water Molecules Nearer to Protein  and deep inside the box ( box size 6 6 6)

There is no way that 70000 water molecules can fit in a 6-nm cubic box; it's 
about an order of magnitude higher than what you achieve with a pure water 
system.  None of this makes any sense to me.  If you need to remove water 
molecules, there are scripts for that:


> When i Try to solvate With Lower Number of Molecules ( 2000 Molcules) Which need to be Kept On either side of Bilayer ,
> Then I need to Continue Shrinking process There by It is  getting Over compressed  ( Area Per Lipid Become Less than Experimental Value)

Certainly if you continue shrinking, you will overcompress the APL.  I would 
suspect that at some point the energy minimization does not produce very good 
results though (high forces and bad energies).

> Also When I solvate with Experimental APL 62A Then My system become over solvated ? How to rectify this Problem

I have never had a problem with a membrane being over-solvated if the APL is 
correct.  Maybe a few stray water molecules, but nothing to the extent you're 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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