Re: [gmx-users] Extend water layer along negative Z-direction

Hi, > The first thing that you need to do is to use editconf to increase your box > z and then genbox to add more solvent. My script (and C-program) do not do > this, they focus only on removing waters that are placed within your > bilayer. Of course it is also trivial to edit the .gro file and c

Re: [gmx-users] essential dynamics analysis

Hi JJ, > 1) Should ED analysis be performed only on the segment of trajectory wherein > the protein's RMSD has equilibrated, am I right?  Because I have the notion > that harmonic analysis of a trajectory can only be performed when the > protein is undergoing fluctuations about a minimum. In other

[gmx-users] Re: Extend water layer along negative Z-direction

Hi ALL, Thanks a lot Chris, Justin and Tsjerk for yor replies. Actually, my problem is not fully resolved. A portion of the protein tail is outside the water box in the Z direction (coordinate in Z is -35). So as suggested by you when I am issuing the command "editconf -f box.gro -o BOX.gro -b