Dear gromacs users, I am simulating interaction of lipid bilayer with some large molecules. I set molecules above the bilayer (upper leaflet) and then released it so that bilayer-molecules interaction was simulated. I am now wondering lower leaflet-molecules interaction, i.e, interaction across Z-boundary, affects on the upper leaflet-molecules interaction causing artificial results.
My question is how many water molecules are you simulating? Now, I am setting 43 waters per lipid molecule, which was determined based on literatures. Is it enough to ensure of periodicity of Z-direction in bilayer simulation? And also, is there any way to determine the enough number of waters? Thank you in advance for you help. Hideya ___________________________________________________________________ Hideya Nakamura, Ph.D. Post Doctoral Associate University of Florida, Particle Engineering Research Center (PERC) _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
