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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
