Hi Taka, I'd say you need to add some more water :) But in addition to that, you definitely should run with pressure coupling in stead of at constant volume.
Cheers, Tsjerk 2009/7/10 H T <takay...@ceres.ocn.ne.jp>: > Hi, I am trying to calculate micelle formation with SDS molecules for > all-atom simulation. > 49 SDS monomers (will increase it later) were settled in 15nm x 15nm x 15nm > box. > And I put water molecules from spc216.gro to the box. > Considering water density is 1g/ml, around 112800 molecules are required but > only 3400 water molecules was settled (around 3%) with genbox command at > maximum. With this configuration, the SDS molecules assemble but also water > cluster appeared. After 100ps MD, there is a room occupied with no atoms > (vacuum, phase separation) and it is a bit funny. (1) Increasing the number > of water to a realistic value or (2) tuning the parameter to avoid spc water > aggregation might be good, but I don't know how to do that. Please give me > a rope for it. Thanks, > > taka > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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/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/mailing_lists/users.php