Dear Justin, Thank you for your previous reply, I am doing Protein-Lipid simulation. After Em When I visualize the str in .vmd The water Molecules Present in Lipid (DPPC) Head groups .There is No Water Molecules Present in the Hydrophobic Part of Bilayer . While The Protein Is in the Center of box .
Then I Have done NVT Equilibration When I visualize the .gro file in vmd Around 40 Water molecules (out of 2699 ) are present in Hydrophobic part of Lipid (that is Moving inside the box, Nearer to protein which is at the center) How to Avoid this ? May I simply delete these 40 water Molecules ? or May I freeze these molecules During NVT Equilibration) ? Can i Leave it as such and Then Proceed Further NPT? I Hope Your Valuable Suggestion? Thanks in Advance -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
