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

vidhya sankar scvsankar_agr at yahoo.com
Sun Oct 28 13:50:30 CET 2012

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) 

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) 

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

I Need to attain Both Correct APL and Solvated with Least  Number of Molecules Only On either side of  Lipid Bilayer   

Thanks In Advance

More information about the gromacs.org_gmx-users mailing list