--- On Fri, 30/3/12, David van der Spoel <sp...@xray.bmc.uu.se> wrote:
> Why are you freezing part of the system? I want a given molecule (20 atoms) to be rigid. Is there a better way that works for any kind of molecule (not just water)? I believe freezing it should be equivalent to keeping it rigid and removing the center of mass motion. > The VAC looks ok doesn't it? How many molecules? My concern is it doesn't look like the typical VAC I find in the literature (as in <http://www.compsoc.man.ac.uk/~lucky/Democritus/Theory/vaf.html>), and I don't know how to quantitatively analyze this function. There are 459 solvent (acetonitrile) molecules. Not too many, I know, but it's box size of ~40 Å. > What is the temperature of your system? Around 295 K. > Is it starting from an equilibrated liquid? Yes, or so I believe. I run a 50 ps equilibration first, and use the resulting checkpoint with -t Thank you, Ignacio -- 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
